Merge branch 'dev' into output-docs-improvements

Author: jfy133

CHANGELOG.md

@@ -13,6 +13,8 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 - [#882](https://github.com/nf-core/eager/pull/882) Define DSL1 execution explicitly, as new versions Nextflow made DSL2 default (♥ to & fix from @Lehmann-Fabian)
 - [#879](https://github.com/nf-core/eager/issues/879) Add missing threads parameter for pre-clipping FastQC for single end data that caused insufficient memory in some cases (♥ to @marcel-keller for reporting)
 - [#885](https://github.com/nf-core/eager/issues/885) Specify task memory for all tools in get_software_versions to account for incompatibilty of java with some SGE clusters causing hanging of the process (♥ to @maxibor for reporting)
+- [#887](https://github.com/nf-core/eager/issues/887) Clarify what is considered 'ultra-short' reads in the help text of clip_readlength, for when you may wish to turn of length filtering during AdapterRemoval (♥ to @TCLamnidis for reporting)
+- [#889](https://github.com/nf-core/eager/issues/889) Remove/updated parameters from benchmarking test profiles (♥ to @TCLamnidis for reporting)
 - [#895](https://github.com/nf-core/eager/issues/895) Output documentation typo fix and added location of output docs in pipeline summary (♥ to @RodrigoBarquera for reporting)
 
 ### `Dependencies`

conf/benchmarking_human.config

@@ -12,26 +12,24 @@ params {
    config_profile_description = "A 'fullsized' benchmarking profile for deepish Human sequencing aDNA data" 
 
    //Input data
-   input = 'https://raw.githubusercontent.com/jfy133/test-datasets/eager/testdata/Benchmarking/benchmarking_human.tsv'
+   input = 'https://raw.githubusercontent.com/nf-core/test-datasets/eager/testdata/Benchmarking/benchmarking_human.tsv'
    // Genome reference
    fasta = 'https://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/hg19.fa.gz'
 
    run_bam_filtering = true
-   bam_discard_unmapped = true
    bam_unmapped_type = 'discard'
    bam_mapping_quality_threshold = 30
 
    dedupper = 'markduplicates'
 
    run_trim_bam = true
-   bamutils_clip_left = 1
-   bamutils_clip_right = 1
+   bamutils_clip_double_stranded_none_udg_left = 1
+   bamutils_clip_double_stranded_none_udg_right = 1
 
    // JAR will need to be downloaded first!
    run_genotyping = true
    genotyping_tool = 'ug'
    genotyping_source = 'trimmed'
-   gatk_ug_jar = 'GenomeAnalysisTK.jar'
    gatk_call_conf = 20
 
    run_sexdeterrmine = true
@@ -41,8 +39,6 @@ params {
    contamination_chrom_name = 'chrX'
 
    run_mtnucratio = true
-
-
 }
 
 process {

conf/benchmarking_vikingfish.config

@@ -20,7 +20,6 @@ params {
    bwaalnl = 1024
 
    run_bam_filtering = true
-   bam_discard_unmapped = true
    bam_unmapped_type = 'discard'
    bam_mapping_quality_threshold = 25
 

nextflow_schema.json

@@ -475,7 +475,7 @@
                     "default": 30,
                     "description": "Specify read minimum length to be kept for downstream analysis.",
                     "fa_icon": "fas fa-ruler",
-                    "help_text": "Defines the minimum read length that is required for reads after merging to be considered for downstream analysis after read merging. Default is `30`.\n\nNote that performing read length filtering at this step is not reliable for correct endogenous DNA calculation, when you have a large percentage of very short reads in your library - such as retrieved in single-stranded library protocols. When you have very few reads passing this length filter, it will artificially inflate your endogenous DNA by creating a very small denominator. In these cases it is recommended to set this to 0, and use `--bam_filter_minreadlength` instead, to filter out 'un-usable' short reads after mapping.\n\n> Modifies AdapterRemoval parameter: `--minlength`\n"
+                    "help_text": "Defines the minimum read length that is required for reads after merging to be considered for downstream analysis after read merging. Default is `30`.\n\nNote that when you have a large percentage of very short reads in your library (< 20 bp) - such as retrieved in single-stranded library protocols - that performing read length filtering at this step is not _always_ reliable for correct endogenous DNA calculation.  When you have very few reads passing this length filter, it will artificially inflate your 'endogenous DNA' value by creating a very small denominator. \n\nIf you notice you have ultra short reads (< 20 bp), it is recommended to set this parameter to 0, and use `--bam_filter_minreadlength` instead, to filter out 'un-usable' short reads after mapping. A caveat, however, is that this will cause a very large increase in computational run time, due to all reads in the library will be being mapped.\n\n> Modifies AdapterRemoval parameter: `--minlength`\n"
                 },
                 "clip_min_read_quality": {
                     "type": "integer",
@@ -1683,7 +1683,7 @@
                 "maltextract_percentidentity": {
                     "type": "number",
                     "description": "Minimum percent identity alignments are required to have to be reported. Recommended to set same as MALT parameter.",
-                    "default": 85.0,
+                    "default": 85,
                     "fa_icon": "fas fa-id-card",
                     "help_text": "Minimum percent identity alignments are required to have to be reported. Higher values allows fewer mismatches between read and reference sequence, but therefore will provide greater confidence in the hit. Lower values allow more mismatches, which can account for damage and divergence of a related strain/species to the reference. Recommended to set same as MALT parameter or higher. Default: `85.0`.\n\nOnly when `--metagenomic_tool malt` is also supplied.\n\n> Modifies MaltExtract parameter: `--minPI`"
                 },