Here is a list of manual tests we can run with the expect output commands
All possible params
skip_preprocessing = false
preprocessing_tool = 'fastp'
preprocessing_skippairmerging = false
preprocessing_excludeunmerged = false
preprocessing_skipadaptertrim = false
preprocessing_adapter1 = null
preprocessing_adapter2 = null
preprocessing_adapterlist = null
preprocessing_minlength = 25
preprocessing_savepreprocessedreads = false
preprocessing_fastp_complexityfilter = false
preprocessing_trim5p = 0 // WARN: slightly different behaviour between fastp & adapterremoval
preprocessing_trim3p = 0 // WARN: slightly different behaviour between fastp & adapterremoval
preprocessing_fastp_complexityfilter_threshold = 30
preprocessing_adapterremoval_preserve5p = false
preprocessing_adapterremoval_adapteroverlap = 1
preprocessing_adapterremoval_skipqualitytrimming = false
preprocessing_adapterremoval_trimbasequalitymin = 20
preprocessing_adapterremoval_skipntrimming = false
preprocessing_adapterremoval_qualitymax = 41
skip_deduplication = false
deduplication_tool = 'markduplicates'
General Combinations (test logging):
-
All numeric values change ✅✅
-
with/without preprocessing ✅✅
-
with/without skipmerging ✅✅
-
with/without merged only ✅✅
-
with/without skip adapter trimming ✅✅
-
with adapterlist ✅✅
-
with custom adapterseq (1&2) ✅✅
-
overriding order of skipping+trim/adapterlist/custom adapterseq ✅✅
-
with default ✅✅
-
with/without preprocessed reads ✅✅
Tool Specific combinations
-
fastp
- with/without complexity filtering ✅
-
AdapterRemoval
- with/without skipqualitytim ✅
- with/without skipntrimming ✅
-
Markduplicates
- With FastP
- SE&PE data ✅
- SE&PE data + preprocessing_excludeunmerged ✅
- PE_only + preprocessing_excludeunmerged ✅
- With AdapterRemoval
- With FastP
- SE&PE data ✅
- SE&PE data + preprocessing_excludeunmerged ✅
- PE_only + preprocessing_excludeunmerged ✅
- With FastP
-
Dedup
- With FastP
- SE&PE data ✅ (expected failure)
- SE&PE data + preprocessing_excludeunmerged ✅ (expected failure)
- PE_only + preprocessing_excludeunmerged ✅
- With AdapterRemoval
- SE&PE data ✅ (expected failure)
- SE&PE data + preprocessing_excludeunmerged ✅ (expected failure)
- PE_only + preprocessing_excludeunmerged ✅
- With FastP
-
Damage Manipulation
-
MapDamage2
- mapdamage2 rescaling with default parameters
- mapdamage2 rescaling with changed parameters
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PMD filtering
- with default parameters
- with stricter threshold
- with fasta masking
- with fasta masking for 1 of 2 references
-
BAM trimming
- with default parameters
- different length by udg treatment
-
All together
-
Library merge
- single reference: no damage manipulation ✅
- single reference: with damage manipulation, on raw data ✅
- single reference: with damage manipulation (trimming), on trimmed data ✅
- single reference: with damage manipulation (pmd + trimming), on pmd filtered data ✅
- multi reference: no damage manipulation ✅
-
-
Sex determination
- With sexdeterrmine
- with default parameters
- With sexdeterrmine
## Test: (1) Two references, only FASTAs ✅
## Expect: Expect all of fai file (x2 SAMTOOLS_FAIDX processes), dict file (x2 PICARD_CREATESEQUENCEDICTIONARY), bwa index directory (x2 BWA_INDEX) etc. to be generated and present in per reference results/reference folder
nextflow run ../main.nf -profile singularity,test --outdir ./results --input samplesheet.tsv --fasta reference_sheet_multiref_test01.csv -ansi-log false -dump-channels --save_reference
## Test: (2) Two reference FASTAs, one also has fai ✅
## Expect: Expect one fai file (x1 SAMTOOLS_FAIDX processes), 2 dict (x2 PICARD_CREATESEQUENCEDICTIONARY), 2 bwa index directory (x2 BWA_INDEX) etc. to be generated and present in per reference results/reference folder
nextflow run ../main.nf -profile singularity,test --outdir ./results --input samplesheet.tsv --fasta reference_sheet_multiref_test02.csv -ansi-log false -dump-channels --save_reference
## Test: (3) Two reference FASTAs, one also has dict ✅
## Expect: Expect two fai file (x2 SAMTOOLS_FAIDX processes), 1 dict file (x1 PICARD_CREATESEQUENCEDICTIONARY), 2 bwa index directory (x2 BWA_INDEX) etc. to be generated and present in per reference results/reference folder
nextflow run ../main.nf -profile singularity,test --outdir ./results --input samplesheet.tsv --fasta reference_sheet_multiref_test03.csv -ansi-log false -dump-channels --save_reference
## Test: (4) Two reference FASTAs, one also has bwa_index ref ✅
## Expect: Expect two fai (x2 SAMTOOLS_FAIDX processes), two dict (x2 PICARD_CREATESEQUENCEDICTIONARY), 1 bwa index directory (x1 BWA_INDEX) etc. to be generated and present in per reference results/reference folder
nextflow run ../main.nf -profile singularity,test --outdir ./results --input samplesheet.tsv --fasta reference_sheet_multiref_test04.csv -ansi-log false -dump-channels --save_reference
## Test: (5) Two reference FASTAs, one also has bowtie2_index ref ✅
## Expect: Expect two fai (x2 SAMTOOLS_FAIDX processes), two dict (x2 PICARD_CREATESEQUENCEDICTIONARY), 1 bowtie2 index directory (x1 BOWTIE2_BUILD) etc. to be generated and present in per reference results/reference folder
nextflow run ../main.nf -profile singularity,test --outdir ./results --input samplesheet.tsv --fasta reference_sheet_multiref_test05.csv -ansi-log false -dump-channels --save_reference --mapping_tool bowtie2
## Test: (6) Mapper index mismatch with `--mapping_tool` (bwa index to bowtie2-align) ✅
## Expect: Expect FAIL at mapping step for Mammoth two fai (x2 SAMTOOLS_FAIDX processes), two dict (x2 PICARD_CREATESEQUENCEDICTIONARY), 1 bowtie2 index directory (BOWTIE2_BUILD) etc. to be generated and present in per reference results/reference folder
nextflow run ../main.nf -profile singularity,test --outdir ./results --input samplesheet.tsv --fasta reference_sheet_multiref_test06.csv -ansi-log false -dump-channels --save_reference --mapping_tool bowtie2
## Test: (7) Mammoth has all pre-supplied ✅
## Expect: Expect one fai (x1 SAMTOOLS_FAIDX processes), one dict (x1 PICARD_CREATESEQUENCEDICTIONARY), 1 bowtie2 index directory (BOWTIE2_BUILD) etc. to be generated and present in per reference results/reference folder
nextflow run ../main.nf -profile singularity,test --outdir ./results --input samplesheet.tsv --fasta reference_sheet_multiref_test07.csv -ansi-log false -dump-channels --save_reference
## Test: (8) No indexing necessary, all already supplied ✅
## Expect: Expect no files to be generated/processes executed, nor results present in per reference results/reference folder
nextflow run ../main.nf -profile singularity,test --outdir ./results --input samplesheet.tsv --fasta reference_sheet_multiref_test08.csv -ansi-log false -dump-channels --save_reference
## Test: (9) All but Human FAI provided ✅
## Expect: Expect one fai (x1 SAMTOOLS_FAIDX processes), and nothing else results/reference folder
nextflow run ../main.nf -profile singularity,test --outdir ./results --input samplesheet.tsv --fasta reference_sheet_multiref_test09.csv -ansi-log false -dump-channels --save_reference
## Test: (10) All but Human dict provided ✅
## Expect: Expect one dict (x1 PICARD_CREATESEQUENCEDICTIONARY processes), and nothing else results/reference folder
nextflow run ../main.nf -profile singularity,test --outdir ./results --input samplesheet.tsv --fasta reference_sheet_multiref_test10.csv -ansi-log false -dump-channels --save_reference
## Test: (11) Broken path correctly fails pipeline ✅
## Expect: Expect fail
nextflow run ../main.nf -profile singularity,test --outdir ./results --input samplesheet.tsv --fasta reference_sheet_multiref_test11.csv -ansi-log false -dump-channels --save_reference
# Test: File input via reference sheet
# Expect: Qualimap with bed, mtnucratio and angsd successful and bedtools not run for hs37d5, qualimap without bed file, mtnucratio and bedtools successful and angsd not run for Mammoth_MT
nextflow run main.nf -profile test_multiref,docker --outdir ./results --run_bedtools_coverage --run_contamination_estimation_angsd --run_mtnucratio## IMPORTANT: CHECK COMMANDS IN BOTH SE/PE EXAMPLES!
## numeric tests: check all numeric parameters are present and match those in the command:
## should also show `--collapse`, and single `_merged` file in dumped channel
## .settings should indicate two adapter sequences on lines 7/8
## check no other results files (i.e., FASTQs) than settings
nextflow run ../main.nf -profile test,singularity --input data/samplesheet.tsv --fasta data/reference/Mammoth_MT_Krause.fasta --outdir ./results -ansi-log false -dump-channels --preprocessing_tool 'adapterremoval' --preprocessing_minlength 30 --preprocessing_trim5p 5 --preprocessing_trim3p 3 --preprocessing_adapterremoval_adapteroverlap 3 --preprocessing_adapterremoval_trimbasequalitymin 25 --preprocessing_adapterremoval_qualitymax 47
## Skip preprocessing: no adapterremoval executed
nextflow run ../main.nf -profile test,singularity --input data/samplesheet.tsv --fasta data/reference/Mammoth_MT_Krause.fasta --outdir ./results -ansi-log false -dump-channels --preprocessing_tool 'adapterremoval' --skip_preprocessing
## Skip merging: command for paired does not have `--collapse`, and a.dump() on preprocessing out shows two FASTQs
nextflow run ../main.nf -profile test,singularity --input data/samplesheet.tsv --fasta data/reference/Mammoth_MT_Krause.fasta --outdir ./results -ansi-log false -dump-channels --preprocessing_tool 'adapterremoval' --preprocessing_skippairmerging
## Merged only: CAT_FASTQ command should only have collapsed and collapsed truncated, no pair1/pair2 truncated
nextflow run ../main.nf -profile test,singularity --input data/samplesheet.tsv --fasta data/reference/Mammoth_MT_Krause.fasta --outdir ./results -ansi-log false -dump-channels --preprocessing_tool 'adapterremoval' --preprocessing_excludeunmerged
## Skip adapter trimming: .command.sh should have adapter1/2 specifies with empty string in quotes adapter sequences in .settings log file should be empty,
nextflow run ../main.nf -profile test,singularity --input data/samplesheet.tsv --fasta data/reference/Mammoth_MT_Krause.fasta --outdir ./results -ansi-log false -dump-channels --preprocessing_tool 'adapterremoval' --preprocessing_skipadaptertrim
## Adapter List: adapterlist file should be present in the command, settings should have multiple sets of 1/2 sadapter sequences
nextflow run ../main.nf -profile test,singularity --input data/samplesheet.tsv --fasta data/reference/Mammoth_MT_Krause.fasta --outdir ./results -ansi-log false -dump-channels --preprocessing_tool 'adapterremoval' --preprocessing_adapterlist 'data/adapterlist_ar.txt'
## Custom adapter trimming sequences: .command.sh should display the input sequences as does the `.settings` file
nextflow run ../main.nf -profile test,singularity --input data/samplesheet.tsv --fasta data/reference/Mammoth_MT_Krause.fasta --outdir ./results -ansi-log false -dump-channels --preprocessing_tool 'adapterremoval' --preprocessing_adapter1 AAAA --preprocessing_adapter2 AAAAAAA
## Check skipping adapter trimming overrides adapterlist/sequences
nextflow run ../main.nf -profile test,singularity --input data/samplesheet.tsv --fasta data/reference/Mammoth_MT_Krause.fasta --outdir ./results -ansi-log false -dump-channels --preprocessing_tool 'adapterremoval' --preprocessing_skipadaptertrim --preprocessing_adapterlist 'data/adapterlist_ar.txt' --preprocessing_adapter1 AAAA --preprocessing_adapter2 AAAAAAA
## Check adapterlist overrides custom sequences
nextflow run ../main.nf -profile test,singularity --input data/samplesheet.tsv --fasta data/reference/Mammoth_MT_Krause.fasta --outdir ./results -ansi-log false -dump-channels --preprocessing_tool 'adapterremoval' --preprocessing_adapterlist 'data/adapterlist_ar.txt' --preprocessing_adapter1 AAAA --preprocessing_adapter2 AAAAAAA
## Check default trimming works: command only contains file and defaults numeric and flag parameters as specified in nextflow.config. Settings file should contain tool-default adapter sequences
nextflow run ../main.nf -profile test,singularity --input data/samplesheet.tsv --fasta data/reference/Mammoth_MT_Krause.fasta --outdir ./results -ansi-log false -dump-channels --preprocessing_tool 'adapterremoval'
## Check saving preprocessed reads: check output directory contains preprocessed FASTQ reads for both files
nextflow run ../main.nf -profile test,singularity --input data/samplesheet.tsv --fasta data/reference/Mammoth_MT_Krause.fasta --outdir ./results -ansi-log false -dump-channels --preprocessing_tool 'adapterremoval' --preprocessing_savepreprocessedreads
## Check quality trimming and trimm n is is turned off: flags should not be in .command.sh and settings should saythey are set as 'No'
nextflow run ../main.nf -profile test,singularity --input data/samplesheet.tsv --fasta data/reference/Mammoth_MT_Krause.fasta --outdir ./results -ansi-log false -dump-channels --preprocessing_tool 'adapterremoval' --preprocessing_adapterremoval_skipqualitytrimming --preprocessing_adapterremoval_skipntrimming## numeric tests: check all numeric parameters are present and match those in the command:
## should also show `-m`, and single `_merged` file in dumped channel for PqE data
## should see warning that --include_unmerged is specified so not dumping to separate file
## .log should indicate two default Illumrina read1/read2 adapter sequences
## should see 'Merged and filtered' section
## check no other results files (i.e., FASTQs) than settings
## Should see command right at the end of log has correct numberic values
nextflow run ../main.nf -profile test,singularity --input data/samplesheet.tsv --fasta data/reference/Mammoth_MT_Krause.fasta --outdir ./results -ansi-log false -dump-channels --preprocessing_tool 'fastp' --preprocessing_minlength 30 --preprocessing_trim5p 5 --preprocessing_trim3p 3
## Skip preprocessing: no adapterremoval executed
nextflow run ../main.nf -profile test,singularity --input data/samplesheet.tsv --fasta data/reference/Mammoth_MT_Krause.fasta --outdir ./results -ansi-log false -dump-channels --preprocessing_tool 'fastp' --skip_preprocessing
## Skip merging: command for paired does not have `-m`, and a.dump() on preprocessing out shows two FASTQs, single end unmodified
nextflow run ../main.nf -profile test,singularity --input data/samplesheet.tsv --fasta data/reference/Mammoth_MT_Krause.fasta --outdir ./results -ansi-log false -dump-channels --preprocessing_tool 'fastp' --preprocessing_skippairmerging
## Merged only: no `--include_unmerged` in .command.sh or log file (and can check merged.fastq.gz is small than default run)
nextflow run ../main.nf -profile test,singularity --input data/samplesheet.tsv --fasta data/reference/Mammoth_MT_Krause.fasta --outdir ./results -ansi-log false -dump-channels --preprocessing_tool 'fastp' --preprocessing_excludeunmerged
## Skip adapter trimming: .command.sh should have --disable_adapter_trimming, and no references to any adapters at the top of the log
nextflow run ../main.nf -profile test,singularity --input data/samplesheet.tsv --fasta data/reference/Mammoth_MT_Krause.fasta --outdir ./results -ansi-log false -dump-channels --preprocessing_tool 'fastp' --preprocessing_skipadaptertrim
## Adapter List: adapterlist file should be present in the command and in command in log... (no other specific stats on this :( ))
nextflow run ../main.nf -profile test,singularity --input data/samplesheet.tsv --fasta data/reference/Mammoth_MT_Krause.fasta --outdir ./results -ansi-log false -dump-channels --preprocessing_tool 'fastp' --preprocessing_adapterlist 'data/adapterlist_fastp.fa'
## Custom adapter trimming sequences: .command.sh should display the input sequences and no 'detected' reads in log; HTML should show AAAA adapters of all lengths or ends of 'detected' adapters
nextflow run ../main.nf -profile test,singularity --input data/samplesheet.tsv --fasta data/reference/Mammoth_MT_Krause.fasta --outdir ./results -ansi-log false -dump-channels --preprocessing_tool 'fastp' --preprocessing_adapter1 AAAA --preprocessing_adapter2 AAAAAAA
## Check saving preprocessed reads: check output directory contains preprocessed FASTQ reads for both files
nextflow run ../main.nf -profile test,singularity --input data/samplesheet.tsv --fasta data/reference/Mammoth_MT_Krause.fasta --outdir ./results -ansi-log false -dump-channels --preprocessing_tool 'fastp' --preprocessing_minlength 30 --preprocessing_trim5p 5 --preprocessing_trim3p 3 --preprocessing_savepreprocessedreads
7d/dd2a00
## Check skippting adapter trimming overrides adapterlist/sequences, i.e. no adapter trimming references in log and --disabled in command!
nextflow run ../main.nf -profile test,singularity --input data/samplesheet.tsv --fasta data/reference/Mammoth_MT_Krause.fasta --outdir ./results -ansi-log false -dump-channels --preprocessing_tool 'fastp' --preprocessing_skipadaptertrim --preprocessing_adapterlist 'data/adapterlist_fastp.fa' --preprocessing_adapter1 AAAA --preprocessing_adapter2 AAAAAAA
## Check adapterlist overrides custom sequences: no custom sequences in log/command, only adapter list (auto-detection allowed)
nextflow run ../main.nf -profile test,singularity --input data/samplesheet.tsv --fasta data/reference/Mammoth_MT_Krause.fasta --outdir ./results -ansi-log false -dump-channels --preprocessing_tool 'fastp' --preprocessing_adapterlist 'data/adapterlist_fastp.fa' --preprocessing_adapter1 AAAA --preprocessing_adapter2 AAAAAAA
## Check default trimming works: command only contains --detect_adpater_for_pe (no other adapter related stuff). Log file should contain tool-default auto-detection (PE only)
nextflow run ../main.nf -profile test,singularity --input data/samplesheet.tsv --fasta data/reference/Mammoth_MT_Krause.fasta --outdir ./results -ansi-log false -dump-channels --preprocessing_tool 'fastp'
## Check complexity filter: in command and in log (should say: reads failed due to low complexity)
nextflow run ../main.nf -profile test,singularity --input data/samplesheet.tsv --fasta data/reference/Mammoth_MT_Krause.fasta --outdir ./results -ansi-log false -dump-channels --preprocessing_tool 'fastp' --preprocessing_fastp_complexityfilter --preprocessing_fastp_complexityfilter_threshold 90## Large Ref: if --fasta_largeref specified, `csi` file generated and published alongisde BAM file; .command.sh contains -c`
nextflow run ../main.nf -profile test,singularity --outdir ./results -resume -dump-channels -ansi-log false --input data/samplesheet.tsv --fasta data/reference/Mammoth_MT_Krause.fasta --fasta_largeref## BWA ALN (with merging): SAMSE run twice, BWA ALN .command.sh read gorup header is not `null` & contains -n -k -l -o values, `.bai` file present in `mapping/` directory
## Samtools flagstat figures & all versions preent in MultiQC report
nextflow run ../main.nf -profile test,singularity --outdir ./results -resume -dump-channels -ansi-log false --input data/samplesheet.tsv --fasta data/reference/Mammoth_MT_Krause.fasta
## BWA ALN (with merging): Both SAMSE and SAMPE executed
nextflow run ../main.nf -profile test,singularity --outdir ./results -resume -dump-channels -ansi-log false --input data/samplesheet.tsv --fasta data/reference/Mammoth_MT_Krause.fasta --preprocessing_skippairmerging
## CircularMapper with reference elongation
## Expect: Reference elongation is ran, and circularmapper SWF is ran.
## Check: Expect the elongated reference and BWA index directory within the `reference` directory. Also 2 bam files together with their BAIs and Flagstats in the `mapping/circularmapper` directory.
nextflow run main.nf -profile test,docker --outdir ./results -w work/ -resume -dump-channels -ansi-log false --fasta_circular_target 'NC_007596.2' --mapping_tool circularmapper --save_reference## CircularMapper with an already elongated reference. Big reference flag. Also check that bwa_aln flags also propagate when using circularmapper.
## Expect: Reference elongation is NOT ran, and circularmapper SWF is ran.
## Check: 2 bam files together with their CSIs and Flagstats in the `mapping/circularmapper` directory.
## Also check the .command.sh for the -k and -n flags during BWA ALN.
nextflow run main.nf -profile test,docker --outdir ./results -w work/ -resume -dump-channels -ansi-log false --fasta_circular_target 'NC_007596.2' --mapping_tool circularmapper --fasta_circularmapper_elongatedfasta data/reference/Mammoth_MT_Krause_500/Mammoth_MT_Krause_500.fasta --fasta_circularmapper_elongatedindex data/reference/Mammoth_MT_Krause_500/bwa --fasta_largeref --mapping_bwaaln_n 0.05 --mapping_bwaaln_k 3## Multiref with circularmapper. reference_sheet_multiref.csv edited to include elongated reference and index from first CM manual test for Mammoth_MT.
## Expect: No elongation for Mammoth MT. Elongation for hs37d5_chr21-MT reference.
## Check: 2 bam files together with their CSIs and Flagstats in the `mapping/circularmapper` directory PER REFERENCE (3 libraries (from 2 samples) x 2 references x 3 files = 18 files total).
## Also, elongated hs37d5_chr21-MT is not saved, since --save_reference was not specified. But it did get elongated.
nextflow run main.nf -profile test_multiref,docker --outdir ./results -w work/ -resume -dump-channels -ansi-log false --fasta_sheet /Users/lamnidis/Software/github/jbv2/eager/data/reference/reference_sheet_multiref.csv --mapping_tool circularmapper --fasta_largeref --mapping_bwaaln_n 0.05 --mapping_bwaaln_k 3## Circularmapper with circularfilter, with a provided elongated reference.
## Expect: No elongation for Mammoth MT.
## Check: 2 bam files together with their CSIs and Flagstats in the `mapping/circularmapper` directory. (6 files total). Ensure files have the @SQ tag of the circular choromosome.
nextflow run main.nf -profile test,docker --outdir ./results -w work/ -resume -dump-channels -ansi-log false --fasta_circular_target 'NC_007596.2' --mapping_tool circularmapper --fasta_circularmapper_elongatedfasta data/reference/Mammoth_MT_Krause_500/Mammoth_MT_Krause_500.fasta --fasta_circularmapper_elongatedindex data/reference/Mammoth_MT_Krause_500/bwa --fasta_largeref --mapping_bwaaln_n 0.05 --mapping_bwaaln_k 3 --mapping_circularmapper_circularfilterAll possible parameters
preprocessing_skippairmerging = true
skip_preprocessing = true
Tests
##Check pair end merged and single end processed correctly
## Expect: host_removal is runned and we have a folder containing filtered gzip fastqs without host reads
## Checked that host_removal folder exists, first mapped read is not in the fastq as: samtools view -F 4 *.bam | head -n 1, and grep for the read name in the fastq
nextflow run ../main.nf -profile docker,test --outdir results_hostremoval -w results_hostremoval/work --run_host_removal
##Check pair end merged and single end processed correctly and host reads in but masked with Ns
## Expect: host_removal is runned and we have a folder containing filtered gzip fastqs with host reads but replaced with Ns
##Checked that the read is masked with: samtools view -F 4 *.bam | head -n 1, and grep for the read name in the fastq
nextflow run ../main.nf -profile docker,test --outdir results_hostremoval_replace -w results_hostremoval_replace/work --run_host_removal --host_removal_mode replace
##Check pair end non-merged and single end processed correctly
## Expect: host_removal is runned and we have a folder containing filtered gzip fastqs without host reads
## Checked that first mapped read is not in the fastq as: samtools view -F 4 *.bam | head -n 1, and grep for the read name in the fastq
nextflow run ../main.nf -profile docker,test --outdir results_hostremoval_skipPEmerging -w results_hostremoval_skipPEmerging/work --run_host_removal --preprocessing_skippairmerging
##Check it still runs when preprocessing is not done and files are proper
## Expect: host_removal is runned and we have a folder containing filtered gzip fastqs without host reads and no preprocessing folder present.
## Checked that first mapped read is not in the fastq as: samtools view -F 4 *.bam | head -n 1, and grep for the read name in the fastq
nextflow run ../main.nf -profile docker,test --outdir results_hostremoval_skipPreprocessing -w results_hostremoval_skipPreprocessing/work --run_host_removal --skip_preprocessing
##Check it runs with multiple lanes and gives correct output per lane
## Expect: host_removal is runned and we have a folder containing filtered gzip fastqs without host reads
## Checked that we obtain all the fastq for all the lanes in the input TSV
## Checked that first mapped read is not in the fastq as: samtools view -F 4 *.bam | head -n 1, and grep for the read name in the fastq
## Checked that the number of reads is not the same as in the original input by counting the number of reads.
nextflow run ../main.nf -profile docker,test --input mammoth_design_fastq_multilane_multilib.tsv --outdir results_hostremoval_multilane_multilib -w results_hostremoval_multilane_multilib/work --run_host_removal
All possible parameters
// BAM Filtering
run_bamfiltering = false
bamfiltering_minreadlength = 0
bamfiltering_mappingquality = 0
bamfiltering_generateunmappedfastq = false
bamfiltering_generatemappedfastq = false
bamfiltering_retainunmappedgenomicbam = false // downstream genomics only
bamfiltering_savefilteredbam = false // can include unmapped reads if --bamfiltering_retainunmappedgenomicbam specified
// Metagenomic Screening
run_metagenomics = false
metagenomics_input = 'unmapped' // mapped, all, unmapped -> mapped vs all specified in SAMTOOLS_FASTQ_MAPPED in modules.conf, unmapped hardcoded SAMTOOLS_FASTQ_UMAPPEDTests
## Check no BAM filtering
## Expect: full completion of pipeline without any bam filtering execution
nextflow run ../main.nf -profile test,singularity --outdir ./results -ansi-log false --input data/samplesheet.tsv --fasta data/reference/Mammoth_MT_Krause.fasta
## Check BAM filtering, mapped reads only in downstream BAM
## Expect to see FILTER_BAM workflow with VIEW and FLAGSTAT, no results directory
nextflow run ../main.nf -profile test,singularity --outdir ./results -ansi-log false --input data/samplesheet.tsv --fasta data/reference/Mammoth_MT_Krause.fasta --run_bamfiltering
## Check BAM filtering, mapped reads only in downstream BAM
## Expect to see FILTER_BAM workflow with VIEW and FLAGSTAT, only quality filtered BAMs in results directory, `samtools view` should show only mapped reads
nextflow run ../main.nf -profile test,singularity --outdir ./results -ansi-log false --input data/samplesheet.tsv --fasta data/reference/Mammoth_MT_Krause.fasta --run_bamfiltering --bamfiltering_savefilteredbams
## Check BAM filtering, mapped reads only in downstream BAM with length filtering
## Expect: to see filtered and length filtered BAM in results dir, `samtools stats` on lengthonly, mapped and unmapped , and grep RL shortest read at 50 and only mapped reads, straight BAM should be both mapped only and RL shortest at 50, multiQC should have flagstats
nextflow run ../main.nf -profile test,singularity --outdir ./results -ansi-log false --input data/samplesheet.tsv --fasta data/reference/Mammoth_MT_Krause.fasta --run_bamfiltering --bamfiltering_savefilteredbams --bamfiltering_minreadlength 50
## Check BAM filtering mapped reads only in downstream BAM, no length filtering, but with quality filtering
## Expect: *filtered.bam, samtools stats has < 50 bp, mapped only and samtools view -q 0 produces reads
## TODO: BEFORE RELEASE UPDATE MULTIQC TO PICK UP BOTH BEFORE AND AFTER FILTERING
nextflow run ../main.nf -profile test,singularity --outdir ./results -ansi-log false --input data/samplesheet.tsv --fasta data/reference/Mammoth_MT_Krause.fasta --run_bamfiltering --bamfiltering_savefilteredbams
## Check BAM filtering mapped reads only in downstream BAM, length filtering and quality filtering
## Expect: *filtered.bam, samtools stats has >= 50 bp, mapped only, and samtools stats MQ0: 0
nextflow run ../main.nf -profile test,singularity --outdir ./results -ansi-log false --input data/samplesheet.tsv --fasta data/reference/Mammoth_MT_Krause.fasta --run_bamfiltering --bamfiltering_savefilteredbams --bamfiltering_minreadlength 50 --bamfiltering_mappingquality 37
## Check BAM filtering without length/quality filtering, with retained unmapped reads in genomic BAM (why would one need this!? But w/e)
## Expect: 'filtered' BAM still contains unmapped reads in samtools stats
nextflow run ../main.nf -profile test,singularity --outdir ./results -ansi-log false --input data/samplesheet.tsv --fasta data/reference/Mammoth_MT_Krause.fasta --run_bamfiltering --bamfiltering_savefilteredbams --bamfiltering_retainunmappedgenomicbam
## Check BAM filtering with length/quality filtering, with retained unmapped reads in genomic BAM
## Expect: filtered and length filtered BAMs, final BAM (not length only) should have min RL of 50, MQO: 0, but retain unmapped reads
nextflow run ../main.nf -profile test,singularity --outdir ./results -ansi-log false --input data/samplesheet.tsv --fasta data/reference/Mammoth_MT_Krause.fasta --run_bamfiltering --bamfiltering_savefilteredbams --bamfiltering_retainunmappedgenomicbam --bamfiltering_minreadlength 50 --bamfiltering_mappingquality 37
## Check BAM filtering with length filtering but no quality filtering, with retained unmapped reads in genomic BAM
## Expect: filtered and length filtered BAMs, final BAM (not length only) should have min RL of 50, MQO: >=1, but and include retain unmapped reads
nextflow run ../main.nf -profile test,singularity --outdir ./results -ansi-log false --input data/samplesheet.tsv --fasta data/reference/Mammoth_MT_Krause.fasta --run_bamfiltering --bamfiltering_savefilteredbams --bamfiltering_retainunmappedgenomicbam --bamfiltering_minreadlength 50
## Check BAM filtering with unmapped FASTQ generation with length/quality filtering of genomic BAM
## Expect: BAM and unmapped FASTQ files in results, samtools stats should have RL >= 50 and MPQ:0
nextflow run ../main.nf -profile test,singularity --outdir ./results -ansi-log false --input data/samplesheet.tsv --fasta data/reference/Mammoth_MT_Krause.fasta --run_bamfiltering --bamfiltering_savefilteredbams --bamfiltering_minreadlength 50 --bamfiltering_mappingquality 37 --bamfiltering_generateunmappedfastq
## Check BAM filtering with mapped FASTQ generation with length/quality filtering of genomic BAM
## Expect: BAM and FASTQ files in results, FASTQ should have more number of reads than the BAM (as fastq should not have length nor quality filtering)
nextflow run ../main.nf -profile test,singularity --outdir ./results -ansi-log false --input data/samplesheet.tsv --fasta data/reference/Mammoth_MT_Krause.fasta --run_bamfiltering --bamfiltering_savefilteredbams --bamfiltering_minreadlength 50 --bamfiltering_mappingquality 37 --bamfiltering_generatemappedfastq
## Check BAM filtering with mapped FASTQ generation WITHOUT length/quality filtering of genomic BAM
## Expect: BAM and FASTQ files in results, FASTQ should have save number of reads as in the BAM
nextflow run ../main.nf -profile test,singularity --outdir ./results -ansi-log false --input data/samplesheet.tsv --fasta data/reference/Mammoth_MT_Krause.fasta --run_bamfiltering --bamfiltering_savefilteredbams --bamfiltering_generatemappedfastq
## Check BAM filtering with unmmaped AND mapped FASTQ generation with length/quality filtering of genomic BAM
## Expect: filtered BAM and mapped AND unmapped FASTQ files, and larger FASTQ unmapped files, and BAM files are length/quality filtered
nextflow run ../main.nf -profile test,singularity --outdir ./results -ansi-log false --input data/samplesheet.tsv --fasta data/reference/Mammoth_MT_Krause.fasta --run_bamfiltering --bamfiltering_savefilteredbams --bamfiltering_minreadlength 50 --bamfiltering_mappingquality 37 --bamfiltering_generateunmappedfastq --bamfiltering_generatemappedfastq
## Check BAM filtering (mapped only/length/quality on genomic bam) with metagenomics screening, with unmapped reads to metagenomics
# Expect: filtered BAM (samtools stats | grep SN total/mapped same), and a dump() on the ch_bam_for_metagenomics channel should report unmapped_other. Nr. of reads in dumped FASTQ should match approx unmmaped reads in results/mapping/*.flagstat
nextflow run ../main.nf -profile test,singularity --outdir ./results -ansi-log false --input data/samplesheet.tsv --fasta data/reference/Mammoth_MT_Krause.fasta --run_bamfiltering --bamfiltering_savefilteredbams --bamfiltering_minreadlength 50 --bamfiltering_mappingquality 37 --run_metagenomics -dump-channels
nextflow run ../main.nf -profile test,singularity --outdir ./results -ansi-log false --input data/samplesheet.tsv --fasta data/reference/Mammoth_MT_Krause.fasta --run_bamfiltering --bamfiltering_savefilteredbams --bamfiltering_minreadlength 50 --bamfiltering_mappingquality 37 --run_metagenomics -dump-channels
## Check BAM filtering (mapped only/length/quality on genomic bam) with metagenomics screening, with mapped only reads going to metagenomics
# Expect: filtered BAM (samtools stats | grep SN total/mapped same), and a dump() on the ch_bam_for_metagenomics channel should report mapped_other. Nr. of reads in dumped FASTQ should match approx mmaped reads in results/mapping/*.flagstat
nextflow run ../main.nf -profile test,singularity --outdir ./results -ansi-log false --input data/samplesheet.tsv --fasta data/reference/Mammoth_MT_Krause.fasta --run_bamfiltering --bamfiltering_savefilteredbams --bamfiltering_minreadlength 50 --bamfiltering_mappingquality 37 --run_metagenomics --metagenomics_input 'mapped' -dump-channels
## Check BAM filtering (mapped only/length/quality on genomic bam) with metagenomics screening, with all reads going to metagenomics
# Expect: filtered BAM (samtools stats | grep SN total/mapped same), and a dump() on the ch_bam_for_metagenomics channel should report mapped_other. Nr. of reads in dumped FASTQ should match total reads in results/mapping/*.flagstat
nextflow run ../main.nf -profile test,singularity --outdir ./results -ansi-log false --input data/samplesheet.tsv --fasta data/reference/Mammoth_MT_Krause.fasta --run_bamfiltering --bamfiltering_savefilteredbams --bamfiltering_minreadlength 50 --bamfiltering_mappingquality 37 --run_metagenomics --metagenomics_input 'all' -dump-channels
## Check BAM filtering NO LENGTH/QAULITY with metagenomics screening, with unmapped reads to metagenomics
# Expect: filtered BAM (samtools stats SN quality average < 36.7 or view -q 0 vs. -q 37 is different and RL reads min <50), and a dump() on the ch_bam_for_metagenomics channel should report mapped_other. Nr. of reads in dumped FASTQ should match unmapped reads as calculated from results/mapping/*.flagstat. Note: No filtered flagstat expected!
nextflow run ../main.nf -profile test,singularity --outdir ./results -ansi-log false --input data/samplesheet.tsv --fasta data/reference/Mammoth_MT_Krause.fasta --run_bamfiltering --bamfiltering_savefilteredbams --run_metagenomics --metagenomics_input 'unmapped' -dump-channels
## Check BAM filtering NO LENGTH/QAULITY with metagenomics screening, with unmapped reads to metagenomics and save unmapped FASTQ
# Expect: filtered BAM (samtools stats SN quality average < 36.7 or view -q 0 vs. -q 37 is different and RL reads min <50), and a dump() on the ch_bam_for_metagenomics channel should report unmapped_other. Nr. of reads in dumped FASTQ should match unmapped reads as calculated from results/mapping/*.flagstat; and unmapped other fASTQ in bam_filtering directoryt. Note: No filtered flagstat expected!
nextflow run ../main.nf -profile test,singularity --outdir ./results -ansi-log false --input data/samplesheet.tsv --fasta data/reference/Mammoth_MT_Krause.fasta --run_bamfiltering --bamfiltering_savefilteredbams --run_metagenomics --metagenomics_input 'unmapped' -dump-channels
## Check BAM filtering NO LENGTH/QAULITY with metagenomics screening, with mapped only reads going to metagenomics
# Expect: filtered BAM (samtools stats SN quality average < 36.7 or view -q 0 vs. -q 37 is different and RL reads min <50), and a dump() on the ch_bam_for_metagenomics channel should report mapped_other. Nr. of reads in dumped FASTQ should be roughly matching mappd reads as calculated from results/mapping/*.flagstatt. Note: No filtered flagstat expected!
nextflow run ../main.nf -profile test,singularity --outdir ./results -ansi-log false --input data/samplesheet.tsv --fasta data/reference/Mammoth_MT_Krause.fasta --run_bamfiltering --bamfiltering_savefilteredbams --run_metagenomics --metagenomics_input 'mapped' -dump-channels
## Check BAM filtering NO LENGTH/QAULITY with metagenomics screening, with all reads going to metagenomics
# Expect: filtered BAM (samtools stats SN quality average < 36.7 or view -q 0 vs. -q 37 is different and RL reads min <50), and a dump() on the ch_bam_for_metagenomics channel should report mapped_other. Nr. of reads in dumped FASTQ should be roughly matching total reads as calculated from results/mapping/*.flagstatt. Note: No filtered flagstat expected!
## Some reads lost, not 100% why command looks OK... but not just unmapped as more than that
nextflow run ../main.nf -profile test,singularity --outdir ./results -ansi-log false --input data/samplesheet.tsv --fasta data/reference/Mammoth_MT_Krause.fasta --run_bamfiltering --bamfiltering_savefilteredbams --run_metagenomics --metagenomics_input 'all' -dump-channels
## Check BAM filtering ONLY length filtering, with metagenomics screening, with unmapped reads to metagenomics and save unmapped FASTQ
## Metagenomics with length only
# Expect: filtered BAM (samtools stats SN quality average < 36.7 or view -q 0 vs. -q 37 is different and RL reads min >= 50), and a dump() on the ch_bam_for_metagenomics channel should report unmapped_other. Nr. of reads in dumped FASTQ should match unmapped reads as calculated from results/mapping/*.flagstat; and unmapped other fASTQ in bam_filtering directoryt.
nextflow run ../main.nf -profile test,singularity --outdir ./results -ansi-log false --input data/samplesheet.tsv --fasta data/reference/Mammoth_MT_Krause.fasta --run_bamfiltering --bamfiltering_savefilteredbams --run_metagenomics --metagenomics_input 'unmapped' -dump-channels --bamfiltering_minreadlength 50
## Check BAM filtering ONLY length filtering, with metagenomics screening, with unmapped reads to metagenomics and save unmapped FASTQ
## Metagenomics with length only
# Expect: filtered BAM (samtools stats SN quality average < 36.7 or view -q 0 vs. -q 37 is not different and RL reads min <= 50), and a dump() on the ch_bam_for_metagenomics channel should report unmapped_other. Nr. of reads in dumped FASTQ should match unmapped reads as calculated from results/mapping/*.flagstat; and unmapped other fASTQ in bam_filtering directoryt.
nextflow run ../main.nf -profile test,singularity --outdir ./results -ansi-log false --input data/samplesheet.tsv --fasta data/reference/Mammoth_MT_Krause.fasta --run_bamfiltering --bamfiltering_savefilteredbams --run_metagenomics --metagenomics_input 'unmapped' -dump-channels --bamfiltering_mappingquality 37
## Check what happens when we do paired-end merging and sending reads to metagenomics...
nextflow run ../main.nf -profile test,singularity --outdir ./results -ansi-log false --input data/samplesheet.tsv --fasta data/reference/Mammoth_MT_Krause.fasta --run_bamfiltering --bamfiltering_savefilteredbams --run_metagenomics --metagenomics_input 'unmapped' -dump-channels --bamfiltering_mappingquality 37 --preprocessing_skippairmergingIn cases where deduplication is expected, check that both mapping and dedup bams exist, and that the latter contains one read less overlapping position NC_007596.2:187-187, where a PCR duplicate exists.
## MARKDUPLICATES with default parameters
## Expect: deduplication directory with bam,bai,flagstat for each library (6 files total). Flagstat for each library should include fewer mapped reads than the mapped bam version. Check that duplicate at NC_007596.2:187-187 is removed.
nextflow run main.nf -profile docker,test --outdir ./results/markduplicates -dump-channels -ansi-log false --deduplication_tool 'markduplicates' -resume
## MARKDUPLICATES run only on merged reads
## Expect: deduplication directory with bam,bai,flagstat for each library (6 files total). Flagstat for each library should include fewer mapped reads than the mapped bam version. Check that duplicate at NC_007596.2:187-187 is removed.
nextflow run main.nf -profile docker,test --outdir ./results/markduplicates_merged -dump-channels -ansi-log false --deduplication_tool 'markduplicates' --preprocessing_excludeunmerged -resume
#### MARKDUPLICATES run only merged only PE
## Use as input a version of the TSV in the test profile that only includes the PE data row.
## Expect: deduplication directory with a single bam,bai,flagstat for the library (3 files total). Flagstat for each library should include fewer mapped reads than the mapped bam version. Check that duplicate at NC_007596.2:187-187 is removed.
nextflow run main.nf -profile docker,test --input ~/eager_dsl2_testing/input/only_PE/pe_only.tsv --outdir ./results/markduplicates_merged_PE_only -dump-channels -ansi-log false --deduplication_tool 'markduplicates' --preprocessing_excludeunmerged -resume#### MARKDUPLICATES with AR on all reads
## Expect: deduplication directory with bam,bai,flagstat for each library (6 files total). Flagstat for each library should include fewer mapped reads than the mapped bam version. Check that duplicate at NC_007596.2:187-187 is removed.
nextflow run main.nf -profile docker,test --outdir ./results/AR_markduplicates -dump-channels -ansi-log false --preprocessing_tool 'adapterremoval' --deduplication_tool 'markduplicates' -resume
#### MARKDUPLICATES with AR on merged reads
## Expect: deduplication directory with bam,bai,flagstat for each library (6 files total). Flagstat for each library should include fewer mapped reads than the mapped bam version. Check that duplicate at NC_007596.2:187-187 is removed.
nextflow run main.nf -profile docker,test --outdir ./results/AR_markduplicates_merged -dump-channels -ansi-log false --preprocessing_tool 'adapterremoval' --deduplication_tool 'markduplicates' --preprocessing_excludeunmerged -resume
#### MARKDUPLICATES with AR on merged reads from PE run only.
## Use as input a version of the TSV in the test profile that only includes the PE data row.
## Expect: deduplication directory with a single bam,bai,flagstat for the library (3 files total). Flagstat for each library should include fewer mapped reads than the mapped bam version. Check that duplicate at NC_007596.2:187-187 is removed.
nextflow run main.nf -profile docker,test --input ~/eager_dsl2_testing/input/only_PE/pe_only.tsv --outdir ./results/AR_markduplicates_merged_PE_only -dump-channels -ansi-log false --preprocessing_tool 'adapterremoval' --deduplication_tool 'markduplicates' --preprocessing_excludeunmerged -resume
#### DEDUP all reads from FastP
## Expect: Run fails with error "Dedup can only be used on collapsed (i.e. merged) PE reads. For all other cases, please set --deduplication_tool to 'markduplicates'."
nextflow run main.nf -profile docker,test --outdir ./results/dedup -dump-channels -ansi-log false --deduplication_tool 'dedup' -resume
#### DEDUP only on merged from FastP
## Expect: Run fails with error "[nf-core] Error: Invalid input/parameter combination: '--deduplication_tool' cannot be 'dedup' on runs that include SE data. Use 'markduplicates' for all or separate SE and PE data into separate runs."
nextflow run main.nf -profile docker,test --outdir ./results/dedup_merged -dump-channels -ansi-log false --deduplication_tool 'dedup' --preprocessing_excludeunmerged -resume
#### DEDUP only on merged from PE runs from FastP
## Use as input a version of the TSV in the test profile that only includes the PE data row.
## Expect: deduplication directory with a single bam,bai,flagstat for the library (3 files total). Flagstat for each library should include fewer mapped reads than the mapped bam version. Check that duplicate at NC_007596.2:187-187 is removed.
nextflow run main.nf -profile docker,test --input ~/eager_dsl2_testing/input/only_PE/pe_only.tsv --outdir ./results/dedup_merged_PE_only -dump-channels -ansi-log false --deduplication_tool 'dedup' --preprocessing_excludeunmerged -resume
#### DEDUP on all reads from Adapter Removal
## Expect: Run fails with error "Dedup can only be used on collapsed (i.e. merged) PE reads. For all other cases, please set --deduplication_tool to 'markduplicates'."
nextflow run main.nf -profile docker,test --outdir ./results/AR_dedup -dump-channels -ansi-log false --preprocessing_tool 'adapterremoval' --deduplication_tool dedup -resume
#### DEDUP only on merged from AdapterRemoval
## Expect: Run fails with error "[nf-core] Error: Invalid input/parameter combination: '--deduplication_tool' cannot be 'dedup' on runs that include SE data. Use 'markduplicates' for all or separate SE and PE data into separate runs."
nextflow run main.nf -profile docker,test --outdir ./results/AR_dedup_merged -dump-channels -ansi-log false --preprocessing_tool 'adapterremoval' --deduplication_tool 'dedup' --preprocessing_excludeunmerged -resume
#### DEDUP only on merged from PE runs from AdapterRemoval
## Use as input a version of the TSV in the test profile that only includes the PE data row.
## Expect: deduplication directory with a single bam,bai,flagstat for the library (3 files total). Flagstat for each library should include fewer mapped reads than the mapped bam version. Check that duplicate at NC_007596.2:187-187 is removed.
nextflow run main.nf -profile docker,test --input ~/eager_dsl2_testing/input/only_PE/pe_only.tsv --outdir ./results/AR_dedup_merged_PE_only -dump-channels -ansi-log false --preprocessing_tool 'adapterremoval' --deduplication_tool 'dedup' --preprocessing_excludeunmerged -resume#### Use bbduk to remove low complexity reads _without_ saving the intermediate files
## Use kraken as example profiler
## Expect: NO additional directory created, but the files in the profiling directory contain the 'complexity' suffix
nextflow run main.nf -profile test_krakenuniq --outdir ./out --run_metagenomics_complexityfiltering --metagenomics_complexity_tool bbduk
#### Use bbduk to remove low complexity reads _with_ saving intermediate files
## Expect: Additional directory created 'metagenomics_screening/complexity_filter/bbduk' containing 'complexity' fastq.gz files and a bbduk.log file for each library
nextflow run main.nf -profile test_krakenuniq --outdir ./out --run_metagenomics_complexityfiltering --metagenomics_complexity_tool bbduk --metagenomics_complexity_savefastq#### Use prinseq to remove low complexity reads _without_ saving the intermediate files
## Expect: NO additional directory created, but the files in the profiling directory contain the 'complexity_good_out' postfix
nextflow run main.nf -profile test_krakenuniq --outdir out --run_metagenomics_complexityfiltering --metagenomics_complexity_tool prinseq
#### Use prinseq to remove low complexity reads _with_ saving the intermediate files
## Expect: Additional directory created 'metagenomics_screening/complexity_filter/prinseq' that contains the fastq files with 'complexity_good_out' postfix and a 'complexity.log' file for each library
nextflow run main.nf -profile test_krakenuniq --outdir out --run_metagenomics_complexityfiltering --metagenomics_complexity_tool prinseq --metagenomics_complexity_savefastq## Run metaphlan with default parameters
## Expect: Directory created 'metagenomics/profiling/metaphlan containing
# _profile.txt, .bowtie2out.txt and .biom.txt for each library
## Expect: 'metaphlan_taxpasta_table.tsv' in 'metagenomics/postprocessing/taxpasta/'
nextflow run main.nf -profile test_metaphlan --outdir out## Run krakenuniq for metagenomics sequence classification, save only report (default)
## Expect: Directory created 'metagenomics/profiling/krakenuniq' that contains one 'krakenuniq.report' file for each analyzed library
## Expect: 'krakenuniq_taxpasta_table.tsv' in 'metagenomics/postprocessing/taxpasta/'
nextflow run main.nf -profile test_krakenuniq --outdir out
## Use krakenuniq for metagenomics sequence classification, save fastq files
## Expect: Directory created 'metagenomics_screening/profiling/krakenuniq' that contains:
# - 'krakenuniq.report' file
# - 'krakenuniq.classified.txt' file
# - 'classified.fastq.gz' file
# - 'unclassified.fastq.gz' file
# for each analyzed library
## Expect: 'taxpasta_table.tsv' in 'metagenomics/postprocessing/taxpasta/'
nextflow run main.nf -profile test_krakenuniq --outdir out --metagenomics_kraken2_savereads --metagenomics_kraken2_savereadclassifications#### Use kraken2 for metagenomics sequence classification, save only report (default)
## Expect: Directory created 'metagenomics/profiling/kraken2' that contains a 'kraken2.report' file
## for each analyzed library
## Expect: 'kraken2_taxpasta_table.tsv' in 'metagenomics/postprocessing/taxpasta/'
nextflow run main.nf -profile test_kraken2 --outdir out
#### Use krakenuniq for metagenomics sequence classification, save also fastq files
## Expect: Directory created 'metagenomics/profiling/kraken2' that contains:
# - 'kraken2.report' file
# - 'kraken2.classifiedreads.txt' file
# - 'classified.fastq.gz' file
# - 'unclassified.fastq.gz' file
# for each analyzed library
## Expect: 'taxpasta_table.tsv' in 'metagenomics/postprocessing/taxpasta/'
nextflow run run main.nf -profile test_kraken2 --outdir out --metagenomics_kraken2_savereads --metagenomics_kraken2_savereadclassifications#### Use MALT for metagenomics sequence classification, save only report (default)
## Expect: Directory created 'metagenomics/profiling/malt' that contains a '.rma6' file for each analyzed library
## and the -malt-run.log files
nextflow run main.nf -profile test_malt --outdir out
#### Use MALT for metagenomics sequence classification, save reads
## Expect: Directory created 'metagenomics/profiling/malt' that contains for each analyzed library:
# - a '.rma6' file
# - a '.blastn.sam' file
# and a the malt-run.log files
nextflow run main.nf -profile test_malt --outdir out --metagenomics_malt_savereads
#### Use MALT for metagenomics sequence classification, use the --metagenomics_malt_group_size flag
## Expect: Directory created 'metagenomics/profiling/malt' that contains for each analyzed library:
# - a '.rma6' file
# - a '.blastn.sam' file
# a concatenated malt-run.log file and for each group a <strandedness>_<group> logfile
nextflow run main.nf -profile test_malt --outdir out --metagenomics_malt_savereads
# Run Malt with missing parameters
# Expect: Exit 1 and informative error message
nextflow run main.nf -profile test_malt --metagenomics_run_postprocessing --outdir out### Create a SummaryTable from the Malt rma6 files
# Expect: A directory 'metagenomics/postprocessing/maltextract/<strandedness>/'
# Expect: A directory 'metagenomics/postprocessing/megan_summaries'
# Expect: 'megan6_taxpasta_table.tsv' in 'metagenomics/postprocessing/taxpasta/'
# Also there will be an AMPS error which occurs if no taxa are found... Thats why it is ignored to no break the pipeline
nextflow run main.nf -profile test_malt --outdir out --metagenomics_run_postprocessing --metagenomics_maltextract_ncbidir NCBI_DIR --metagenomics_maltextract_taxonlist TAXONLISTFILE
# for generating test data
mkdir testing && cd testing
wget https://raw.githubusercontent.com/nf-core/test-datasets/eager/reference/Mammoth/Mammoth_MT_Krause.fasta
git clone https://github.com/rhuebler/HOPS.git
cd HOPS/Test_Data/Test_Database
unzip table0.db.zip
unzip table0.idx.zip
cd ../../..
mkdir test_data && cd test_data
curl -L ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR895/000/ERR8958750/ERR8958750_1.fastq.gz -o ERR8958750_1.fastq.gz
curl -L ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR895/000/ERR8958750/ERR8958750_2.fastq.gz -o ERR8958750_2.fastq.gz
curl -L ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR895/001/ERR8958751/ERR8958751_1.fastq.gz -o ERR8958751_1.fastq.gz
curl -L ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR895/001/ERR8958751/ERR8958751_2.fastq.gz -o ERR8958751_2.fastq.gz
curl -L ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR895/002/ERR8958752/ERR8958752_1.fastq.gz -o ERR8958752_1.fastq.gz
curl -L ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR895/002/ERR8958752/ERR8958752_2.fastq.gz -o ERR8958752_2.fastq.gz
curl -L ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR895/003/ERR8958753/ERR8958753_1.fastq.gz -o ERR8958753_1.fastq.gz
curl -L ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR895/003/ERR8958753/ERR8958753_2.fastq.gz -o ERR8958753_2.fastq.gz
curl -L ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR895/004/ERR8958754/ERR8958754_1.fastq.gz -o ERR8958754_1.fastq.gz
curl -L ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR895/004/ERR8958754/ERR8958754_2.fastq.gz -o ERR8958754_2.fastq.gz
ls -1 | while read file; do
zcat $file | head -n 4000 > ${file}_reduced.fastq
gzip ${file}_reduced.fastq
done
cd ..
echo "sample_id library_id lane colour_chemistry pairment strandedness damage_treatment r1 r2 bam bam_reference_id
HOP001 ERR8958750 0 4 paired double half /workspace/eager/testing/test_data/ERR8958750_1.fastq.gz_reduced.fastq.gz /workspace/eager/testing/test_data/ERR8958750_2.fastq.gz_reduced.fastq.gz NA NA
HOP001 ERR8958751 0 2 paired double half /workspace/eager/testing/test_data/ERR8958751_1.fastq.gz_reduced.fastq.gz /workspace/eager/testing/test_data/ERR8958751_2.fastq.gz_reduced.fastq.gz NA NA
HOP001 ERR8958752 0 2 paired double half /workspace/eager/testing/test_data/ERR8958752_1.fastq.gz_reduced.fastq.gz /workspace/eager/testing/test_data/ERR8958752_2.fastq.gz_reduced.fastq.gz NA NA
HOP001 ERR8958753 0 2 paired double half /workspace/eager/testing/test_data/ERR8958753_1.fastq.gz_reduced.fastq.gz /workspace/eager/testing/test_data/ERR8958753_2.fastq.gz_reduced.fastq.gz NA NA
HOP001 ERR8958754 0 2 paired double none /workspace/eager/testing/test_data/ERR8958754_1.fastq.gz_reduced.fastq.gz /workspace/eager/testing/test_data/ERR8958754_2.fastq.gz_reduced.fastq.gz NA NA" | sed 's/NA/ /g' | sed 's/ /\t/g' > test.tsv
nextflow run ../main.nf -profile docker \
--input test.tsv \
--outdir ./out \
--run_metagenomics \
--metagenomics_profiling_tool malt \
--metagenomics_profiling_database /workspace/eager/testing/HOPS/Test_Data/Test_Database/ \
--metagenomics_run_postprocessing \
--metagenomics_maltextract_ncbidir HOPS/Resources \
--metagenomics_maltextract_taxonlist HOPS/Resources/default_list.txt \
--fasta Mammoth_MT_Krause.fasta \
--skip_damage_calculation \
--skip_qualimap \
--metagenomics_malt_group_size 3nextflow run main.nf -profile docker
--input testing/test.tsv
--outdir ./out
--run_metagenomics
--metagenomics_profiling_tool kraken2
--metagenomics_profiling_database /workspace/eager/testing/eager_test.tar.gz
--preprocessing_skippairmerging
All possible paramters
// BAM Filtering
params.run_bamfiltering
//Deduplication
params.skip_deduplication
Tests
##Check if mapping + filtering + deduplication is done, meaning params.run_bamfiltering is true and params.skip_deduplication is false
##Expect: a json for each of the of the libraries with all the stats calculates (percent on target raw, percent on target modified, percent on target postdedup, clonality and percent duplicates)
##Checked: there is 3 jsons with all the stats calculates
nextflow run ../main.nf -profile docker,test --outdir results_endorspy_all -w results_endorspy_all/work --run_bamfiltering
##Check if mapping only has been performed, meaning params.run_bamfiltering is false and params.skip_deduplication is true
##Expect: a json for each of the of the libraries with only percent on target raw
##Checked: there is 3 jsons with only Percent on target (%)
nextflow run ../main.nf -profile docker,test --outdir results_endorspy_map_only -w results_endorspy_map_only/work --skip_deduplication --run_bamfiltering false
##Check if mapping and run_bamfiltering done but no dedepup, meaning params.run_bamfiltering is true and params.skip_deduplication is true
##Checked: there is 3 jsons with only Percent on target (%) and Percent on target modified (%) calculated
nextflow run ../main.nf -profile docker,test --outdir results_endorspy_map_filtering_nodedup -w results_endorspy_map_filtering_nodedup/work --run_bamfiltering --skip_deduplication
##Check if mapping and dedup done but no bam filtering, meaning params.run_bamfiltering is false and params.skip_deduplication is true
##Checked: there is 3 jsons with Percent on target (%), Percent on target postdedup (%), Clonality and Percent Duplicates (%)
nextflow run ../main.nf -profile docker,test --outdir results_endorspy_map_nofiltering_dedup -w results_endorspy_map_nofiltering_dedup/work --run_bamfiltering false
##Check if mapping + filtering + deduplication is done (meaning params.run_bamfiltering is true and params.skip_deduplication is false) and multiple reference used
##Expect: a json for each of the of the libraries with all the stats calculates (percent on target raw, percent on target modified, percent on target postdedup, clonality and percent duplicates) for each of the references
##Checked: there is 6 jsons with all the stats calculates: one for each of the references (2) for each of the samples (3 samples in total). All the stats were calculated.
nextflow run ../main.nf -profile docker,test_multiref --outdir results_endorspy_all_multiref -w results_endorspy_all_multiref/work --run_bamfiltering
## DamageProfiler with default parameters
## Expect:damageprofiler directory with txt, pdf, svg for each library (19 files total per library).
nextflow run main.nf -profile test,conda --outdir ./results -resume## mapDamage2 with default parameters
## Expect: mapdamage directory with 3pGtoA_freq, 5pCtoT_freq, dnacomp_genome, dnacomp, Fragmisincorporation_plot, Length_plot, lgdistribution, misincorporation, Runtime_log
nextflow run main.nf -profile test,docker --outdir ./results --damagecalculation_tool mapdamage## mapDamage2 with downsampling to 100 reads
## Expect: mapdamage directory with 3pGtoA_freq, 5pCtoT_freq, dnacomp_genome, dnacomp, Fragmisincorporation_plot, Length_plot, lgdistribution, misincorporation, Runtime_log
nextflow run main.nf -profile test,docker --outdir ./results --damagecalculation_tool mapdamage --damagecalculation_mapdamage_downsample 100## ANGSD contamination estimation with default parameters
## Expect: contamination_estimation/angsd directory with txt for each library and 'nuclear_contamination.txt' summary table.
nextflow run main.nf -profile test,humanbam --outdir ./results --run_contamination_angsd -resume
## ANGSD contamination estimation with quality filters reduced
## Expect: contamination_estimation/angsd directory with txt for each library and 'nuclear_contamination.txt' summary table.
nextflow run main.nf -profile test,humanbam --outdir ./results --run_contamination_angsd --angsd_minq 0 --angsd_mapq 0 -resume## Rescaling with default parameters
## Expect: damage_manipulation directory with a bam and bai per library (4 files total, cause one sample is full UDG), and 2 results_* directories with 6 Stats_out_MCMC_* files each.
nextflow run . -profile test,docker --run_mapdamage_rescaling -resume --outdir ./results
## Rescaling with changed rescale lengths
## Expect: damage_manipulation directory with a bam and bai per library (4 files total, cause one sample is full UDG), and 2 results_* directories with 6 Stats_out_MCMC_* files each.
## Commands checked to ensure parameter gets propagated (Yes, together with default --seq-length of 12.)
nextflow run . -profile test,docker --run_mapdamage_rescaling --damage_manipulation_rescale_length_5p 3 --damage_manipulation_rescale_length_3p 3 -resume --outdir ./results## PMD filtering with default parameters
## Expect: damage_manipulation directory with a bam and bai and flagstat per library (9 files total).
nextflow run . -profile test,docker --run_pmd_filtering -resume --outdir ./results
## number of reads in each file after filtering:
# JK2782_JK2782_TGGCCGATCAACGA_BAM_pmdfiltered.bam: 70
# JK2782_JK2782_TGGCCGATCAACGA_pmdfiltered.bam: 180
# JK2802_JK2802_AGAATAACCTACCA_pmdfiltered.bam: 55
## PMD filtering with changed parameters
## Expect: damage_manipulation directory with a bam and bai and flagstat per library (9 files total). Commands checked to ensure parameter gets propagated.
nextflow run . -profile test,docker --run_pmd_filtering -resume --outdir ./results --damage_manipulation_pmdtools_threshold 4
## number of reads in each file after filtering:
# JK2782_JK2782_TGGCCGATCAACGA_BAM_pmdfiltered.bam: 64
# JK2782_JK2782_TGGCCGATCAACGA_pmdfiltered.bam: 137
# JK2802_JK2802_AGAATAACCTACCA_pmdfiltered.bam: 30## PMD filtering with fasta masking
## Expect: damage_manipulation directory with *.masked.fa and bam and bai and flagstat per library
nextflow run . -profile test_humanbam,docker --run_pmd_filtering --damage_manipulation_pmdtools_reference_mask https://raw.githubusercontent.com/nf-core/test-datasets/eager/reference/Human/1240K.pos.list_hs37d5.0based.bed.gz -resume --outdir ./results## PMD filtering with fasta masking for 1 of 2 references
## Expect: damage_manipulation directory with hs37d5_chr21-MT.masked.fa and bam and bai and flagstat per library and reference (22 files total). hs37d5_chr21-MT first masked with 1240K.pos.list_hs37d5.0based.bed.gz from reference sheet, PMD filtering run with masked reference fasta for hs37d5 and non-masked reference fasta for Mammoth_MT
nextflow run . -profile test_multiref,docker --run_pmd_filtering --outdir ./results## BAM trimming with default parameters (0bp trim)
## Expect: damage_manipulation directory with a bam and bai per library. No trimming actually done. (6 files total. full UDG still goes through module but trimming is 0bp)
nextflow run . -profile test,docker --run_trim_bam -resume --outdir ./results
## BAM trimming with changed parameters
## Expect: damage_manipulation directory with a bam and bai per library. Trimming is done. 0 bp for full UDG, 1-2bp for half, 5-7 for none. (6 files total)
## Giving different on each side to make sure arguments are passed correctly.
nextflow run . -profile test,docker \
-resume \
--outdir ./results \
--run_trim_bam \
--damage_manipulation_bamutils_trim_double_stranded_none_udg_left 5 \
--damage_manipulation_bamutils_trim_double_stranded_none_udg_right 7 \
--damage_manipulation_bamutils_trim_double_stranded_half_udg_left 1 \
--damage_manipulation_bamutils_trim_double_stranded_half_udg_right 2## All together with default parameters + non-0 trimming.
## Expect: damage_manipulation directory with _pmdfiltered, and _pmdfiltered_trimmed bams and bai per library, plus pmd_filtered flagstat files. (5 * 3 = 15 files total).
## Also _rescaled bam/bai for libraries that are not full-UDG. (15 + 4 = 19 files total), and 2 results_* directories with 6 Stats_out_MCMC_* files each.
## Number of reads in each file after trimming should match filtered flagstat.
nextflow run . -profile test,docker \
-resume \
--outdir ./results \
--run_mapdamage_rescaling \
--run_pmd_filtering \
--run_trim_bam \
--damage_manipulation_bamutils_trim_double_stranded_none_udg_left 5 \
--damage_manipulation_bamutils_trim_double_stranded_none_udg_right 7 \
--damage_manipulation_bamutils_trim_double_stranded_half_udg_left 1 \
--damage_manipulation_bamutils_trim_double_stranded_half_udg_right 2## Library merge on single reference, no damage manipulation.
## EXPECT: 1 bam.bai/flagstat set per sample/reference combination. 6 files total.
## Check the headers of the bams to ensure that the correct number of bams are merged (1 for JK2802, 2 for JK2782).
## Also, check that the bams merged are the deduplication output.
## NOTE: JK2782 seems to have some PG tags repeated, as they apply to each input file separately.
nextflow run main.nf -profile test,docker --outdir ./results -w work/ -resume --genotyping_source 'raw' -ansi-log false -dump-channels## Library merge on single reference, merge trimmed bams.
## EXPECT: 1 bam.bai/flagstat set per sample/reference combination. 6 files total.
## Check the headers of the bams to ensure that the correct number of bams are merged (1 for JK2802, 2 for JK2782).
## Also, check that the bams merged are trimmed. (JK2802 is full udg, but header confirms merged bam is "trimmed")
## NOTE: JK2782 seems to have some PG tags repeated, as they apply to each input file separately.
nextflow run main.nf -profile test,docker --outdir ./results -w work/ -resume --genotyping_source 'trimmed' -ansi-log false -dump-channels \
--run_trim_bam \
--damage_manipulation_bamutils_trim_double_stranded_none_udg_left 5 \
--damage_manipulation_bamutils_trim_double_stranded_none_udg_right 7 \
--damage_manipulation_bamutils_trim_double_stranded_half_udg_left 1 \
--damage_manipulation_bamutils_trim_double_stranded_half_udg_right 2## Library merge on single reference, merge pmd bams. Trimming ran but not used downstream.
## EXPECT: 1 bam.bai/flagstat set per sample/reference combination. 6 files total.
## Check the headers of the bams to ensure that the correct number of bams are merged (1 for JK2802, 2 for JK2782).
## Also, check that the bams merged are the pmd ones.
## NOTE: JK2782 seems to have some PG tags repeated, as they apply to each input file separately.
nextflow run main.nf -profile test,docker --outdir ./results -w work/ -resume --genotyping_source 'pmd' -ansi-log false -dump-channels \
--run_trim_bam \
--run_pmd_filtering \
--damage_manipulation_bamutils_trim_double_stranded_none_udg_left 5 \
--damage_manipulation_bamutils_trim_double_stranded_none_udg_right 7 \
--damage_manipulation_bamutils_trim_double_stranded_half_udg_left 1 \
--damage_manipulation_bamutils_trim_double_stranded_half_udg_right 2## Library merge on multi reference. No damage manipulation.
## EXPECT: 1 bam.bai/flagstat set per sample/reference combination. 15 files total. (2 refs * 2 samples * 3 files) + BAM input only on one reference (+3)
## Check the headers of the bams to ensure that the correct number of bams are merged (1 for JK2802, 2 for JK2782).
## Also, check that the bams merged are the dedupped ones.
## NOTE: PG tags are repeated for each chromosome in the reference, times each library! Maybe there's some flag missing from samtools MERGE runs?
nextflow run main.nf -profile test_multiref,docker --outdir ./results -w work/ -resume --genotyping_source 'raw' -ansi-log false -dump-channels## Running sex determination subworkflow from deduplicated bams
## Expect: sex_deterrmine/sexdeterrmine directory with tsv summary table for all individuals.
nextflow run main.nf -profile test_humanbam,arm,docker --outdir ./results --run_sexdeterrmineThese tests were ran before library merging was implemented.
## Gatk UG on raw reads
## Expect: One VCF + .tbi index per sample/reference combination. Also 1 bcftools_stats file per VCF. Additional IR/ subdirectory with 1 bam and 1 bai per sample/reference combination.
nextflow run main.nf -profile test,docker --outdir ./results -w work/ -resume --run_genotyping --genotyping_tool 'ug' --genotyping_source 'raw' --genotyping_gatk_ug_keeprealignbam -ansi-log false -dump-channels## Gatk UG on trimmed reads. Skip bcftools stats.
## Expect: One VCF + .tbi index per sample/reference combination, based on the trimmed bams (this actually shows on the IndelRealigner step and not the UG step). No IR directory. No bcftools_stats file per VCF.
## Checked that the input bam for the UG jobs indeed had trimmed reads. (The full UDG sample has untrimmed bams.)
nextflow run main.nf -profile test,docker --outdir ./results -w work/ -resume --run_genotyping --genotyping_tool 'ug' --genotyping_source 'trimmed' -ansi-log false -dump-channels --skip_bcftools_stats \
--run_trim_bam \
--damage_manipulation_bamutils_trim_double_stranded_none_udg_left 5 \
--damage_manipulation_bamutils_trim_double_stranded_none_udg_right 7 \
--damage_manipulation_bamutils_trim_double_stranded_half_udg_left 1 \
--damage_manipulation_bamutils_trim_double_stranded_half_udg_right 2## Gatk UG on pmd-filtered reads
## Expect: One VCF + .tbi index per sample/reference combination, based on the pmd-filtered bams (this actually shows on the IndelRealigner step and not the UG step). No IR directory. Also 1 bcftools_stats file per VCF.
nextflow run main.nf -profile test,docker --outdir ./results -w work/ -resume --run_genotyping --genotyping_tool 'ug' --genotyping_source 'pmd' -ansi-log false -dump-channels --run_pmd_filtering
## Checked that the bams had fewer reads compared to the raw bams.## Gatk UG on rescaled reads
## Expect: One VCF + .tbi index per sample/reference combination, based on the rescaled bams (this actually shows on the IndelRealigner step and not the UG step). No IR directory. Also 1 bcftools_stats file per VCF.
nextflow run main.nf -profile test,docker --outdir ./results -w work/ -resume --run_genotyping --genotyping_tool 'ug' --genotyping_source 'rescaled' -ansi-log false -dump-channels --run_mapdamage_rescaling## Gatk UG on raw reads, multiple references
## NOTE: Actually fails due to header of BAM input in test_multiref not matching sequences in fasta (which was shortened to chr 21+ for brevity). Provided alternative input without a BAM input line. ( head -n 5 on https://raw.githubusercontent.com/nf-core/test-datasets/eager/testdata/Mammoth/samplesheet_multilane_multilib.tsv ). It then worked fine.
## Expect: One VCF + .tbi index per sample/reference combination. Also 1 bcftools_stats file per VCF. Additional IR/ subdirectory with 1 bam and 1 bai per sample/reference combination.
nextflow run main.nf -profile test_multiref,docker --input test/samplesheet_multilane_multilib_noBAM.tsv --outdir ./results -w work/ -resume --run_genotyping --genotyping_tool 'ug' --genotyping_source 'raw' --genotyping_gatk_ug_keeprealignbam -ansi-log false -dump-channels## Gatk HC on raw reads
## Expect: One VCF + .tbi index per sample/reference combination. Also 1 bcftools_stats file per VCF.
nextflow run main.nf -profile test,docker --outdir ./results -w work/ -resume --run_genotyping --genotyping_tool 'hc' --genotyping_source 'raw' -ansi-log false -dump-channels## Attempt to run Gatk HC on trimmed reads, without activating trimming.
## Expect: FAILURE. Cannot set genotyping source to ;trimmed' without trimming.
nextflow run main.nf -profile test,docker --outdir ./results -w work/ -resume --run_genotyping --genotyping_tool 'hc' --genotyping_source 'trimmed' -ansi-log false -dump-channels --skip_bcftools_stats \
--genotyping_gatk_hc_emitrefconf 'BP_RESOLUTION' \
--genotyping_gatk_hc_out_mode 'EMIT_ALL_ACTIVE_SITES'## Gatk HC on trimmed reads, with different out mode and emit confidence. Skip bcftools stats.
## Expect: One VCF + .tbi index per sample/reference combination.
## Checked .command.sh for correct args.
nextflow run main.nf -profile test,docker --outdir ./results -w work/ -resume --run_genotyping --genotyping_tool 'hc' --genotyping_source 'trimmed' --run_trim_bam -ansi-log false -dump-channels --skip_bcftools_stats \
--genotyping_gatk_hc_emitrefconf 'BP_RESOLUTION' \
--genotyping_gatk_hc_out_mode 'EMIT_ALL_ACTIVE_SITES'## Gatk HC on raw reads, multiple references
## NOTE: Actually fails due to header of BAM input in test_multiref not matching sequences in fasta (which was shortened to chr 21+ for brevity). Provided alternative input without a BAM input line. ( head -n 5 on https://raw.githubusercontent.com/nf-core/test-datasets/eager/testdata/Mammoth/samplesheet_multilane_multilib.tsv ). It then worked fine.
## Expect: One VCF + .tbi index per sample/reference combination . Also 1 bcftools_stats file per VCF.
nextflow run main.nf -profile test_multiref,docker --input test/samplesheet_multilane_multilib_noBAM.tsv --outdir ./results -w work/ -resume --run_genotyping --genotyping_tool 'hc' --genotyping_source 'raw' --genotyping_gatk_ug_keeprealignbam -ansi-log false -dump-channels## Freebayes on raw reads
## Expect: One VCF + .tbi index per sample/reference combination. Also 1 bcftools_stats file per VCF.
nextflow run main.nf -profile test,docker --outdir ./results -w work/ -resume --run_genotyping --genotyping_tool 'freebayes' --genotyping_source 'raw' -ansi-log false -dump-channels## Freebayes on trimmed reads. Different options, and skip bcftools stats.
## Expect: One VCF + .tbi index per sample/reference combination.
## Checked .command.sh for correct args.
nextflow run main.nf -profile test,docker --outdir ./results -w work/ -resume --run_genotyping --genotyping_tool 'freebayes' --genotyping_source 'trimmed' -ansi-log false -dump-channels --skip_bcftools_stats \
--run_trim_bam \
--genotyping_freebayes_skip_coverage 10 \
--genotyping_freebayes_min_alternate_count 2 \
--genotyping_freebayes_ploidy 1## Freebayes on raw reads, multiple references
## Freebayes does not complain about the BAM header not matching the reference.
## Expect: One VCF + .tbi index per sample/reference combination. BAM input only has 1 output for the specified reference. Also 1 bcftools_stats file per VCF.
nextflow run main.nf -profile test_multiref,docker --outdir ./results -w work/ -resume --run_genotyping --genotyping_tool 'freebayes' --genotyping_source 'raw' --genotyping_gatk_ug_keeprealignbam -ansi-log false -dump-channels## Pileupcaller on raw reads. No bed or snp file provided.
## Expect: NO GENOTYPING. PileupCaller requires a bed file and a snp file. Throws an error and stops.
## NOTE: if --fasta is a tsv/csv, then the error is deferred to AFTER parsing and indexing the references.
nextflow run main.nf -profile test,docker --outdir ./results -w work/ -resume --run_genotyping --genotyping_tool 'pileupcaller' --genotyping_source 'raw' -ansi-log false -dump-channels## Pileupcaller on raw reads.
## Expect: One geno/snp/ind/coverage tsv combination per reference (provided that a bed and snp file are present for the reference). geno and snp have same number of lines as SNPs in provided snpfile (977). ind has same number of lines as number of samples (2). Coverage tsv has same lines as ind + 1 for header (3).
nextflow run main.nf -profile test_humanbam,docker --outdir ./results -w work/ -resume --run_genotyping --genotyping_tool 'pileupcaller' --genotyping_source 'raw' -ansi-log false -dump-channels## PileupCaller on raw reads
## Something is wrong with the test input BAM, that makes samtools mpileup fail. samtools quickcheck does not identify a problem, but empty mpileups are generated when the BAM input is included in as an input.
## Expect: One geno/snp/ind/coverage tsv combination per reference (provided that a bed and snp file are present for the reference). geno and snp have same number of lines as SNPs in provided snpfile (977). ind has have same number of lines as number of samples (2). Coverage tsv has same lines as ind + 1 for header (3).
## Specifically, no geno/snp/ind for the reference that has no bed/snp file (Mammoth). Only data for "human" reference.
nextflow run main.nf -profile test_multiref,docker --input test/samplesheet_multilane_multilib_noBAM.tsv --outdir ./results -w work/ -resume --run_genotyping --genotyping_tool 'pileupcaller' --genotyping_source 'raw' -ansi-log false -dump-channels## ANGSD on raw reads. Default parameters. (--genotyping_angsd_glmodel 'samtools' --genotyping_angsd_glformat 'binary' )
## Expect: One `glf.gz` file in binary format per reference.
nextflow run main.nf -profile test,docker --outdir ./results -w work/ -resume --run_genotyping --genotyping_tool 'angsd' --genotyping_source 'raw' -ansi-log false -dump-channels## ANGSD on raw reads. gatk model, beagle binary format.
## Expect: One `beagle.gz` file in beagle format per reference.
nextflow run main.nf -profile test,docker --outdir ./results -w work/ -resume --run_genotyping --genotyping_tool 'angsd' --genotyping_angsd_glmodel 'gatk' --genotyping_angsd_glformat 'beagle_binary' --genotyping_source 'raw' -ansi-log false -dump-channels## ANGSD on raw reads. soapSNP model, binary_three format.
## Expect: One `glf.gz` file in binary_three format per reference.
nextflow run main.nf -profile test,docker --outdir ./results -w work/ -resume --run_genotyping --genotyping_tool 'angsd' --genotyping_angsd_glmodel 'soapsnp' --genotyping_angsd_glformat 'binary_three' --genotyping_source 'raw' -ansi-log false -dump-channels## ANGSD on raw reads. syk model, text format.
## Expect: One `glf.gz` file in binary_three format per reference.
nextflow run main.nf -profile test,docker --outdir ./results -w work/ -resume --run_genotyping --genotyping_tool 'angsd' --genotyping_angsd_glmodel 'syk' --genotyping_angsd_glformat 'text' --genotyping_source 'raw' -ansi-log false -dump-channels## BAM input converted to FastQ and remapped.
## Expect: BAM input shows up in FastQC -> mapping results.
nextflow run main.nf -profile test,docker --outdir ./results -w work/ --convert_inputbam --skip_deduplication -resume -ansi-log false -dump-channels#### MTDNA HAPLOGROUP CLASSIFICATION with default settings
## Expect: Directory created 'mtdna_haplogroup/<reference>/<sample_id>' containing a .txt file for each sample with haplogroup assignments
## Expect: The haplogroup .txt file contains at minimum columns for rank, name, quality, range, and details of the haplogroup assignment
nextflow run main.nf -profile docker,test --outdir ./results/mtdna_haplogroup_test --run_genotyping --genotyping_tool ug --genotyping_source raw --run_classify_mtdna_haplogroup -resume
#### MTDNA HAPLOGROUP CLASSIFICATION with specific arguments
## Expect: Directory created 'mtdna_haplogroup/<reference>/<sample_id>' containing a .txt file for each sample with haplogroup assignments
## Expect: The haplogroup assignment may differ based on the classification settings
nextflow run main.nf -profile docker,test --outdir ./results/mtdna_haplogroup_test --run_classify_mtdna_haplogroup --run_genotyping --genotyping_tool ug --genotyping_source raw --run_classify_mtdna_haplogroup --human_mtdna_reference rsrs --human_mtdna_phylotree phylotree-rsrs@1.0 -resume