Merge pull request #865 from nf-core/dev

Patch Release 2.4.3

Author: jfy133

.github/workflows/ci.yml

@@ -37,13 +37,13 @@ jobs:
 
       - name: Build new docker image
         if: env.MATCHED_FILES
-        run: docker build --no-cache . -t nfcore/eager:2.4.2
+        run: docker build --no-cache . -t nfcore/eager:2.4.3
 
       - name: Pull docker image
         if: ${{ !env.MATCHED_FILES }}
         run: |
           docker pull nfcore/eager:dev
-          docker tag nfcore/eager:dev nfcore/eager:2.4.2
+          docker tag nfcore/eager:dev nfcore/eager:2.4.3
 
       - name: Install Nextflow
         env:
@@ -119,7 +119,7 @@ jobs:
           nextflow run ${GITHUB_WORKSPACE} -profile test,docker --mapper 'circularmapper' --circulartarget 'NC_007596.2'
       - name: MAPPER_BWAMEM Test running with BWA Mem
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --mapper 'bwamem'
+          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --mapper 'bwamem' --skip_collapse
       - name: MAPPER_BT2 Test running with BowTie2
         run: |
           nextflow run ${GITHUB_WORKSPACE} -profile test,docker --mapper 'bowtie2' --bt2_alignmode 'local' --bt2_sensitivity 'sensitive' --bt2n 1 --bt2l 16 --bt2_trim5 1 --bt2_trim3 1
@@ -201,6 +201,10 @@ jobs:
       - name: METAGENOMIC Run the basic pipeline but with unmapped reads going into Kraken
         run: |
           nextflow run ${GITHUB_WORKSPACE} -profile test_tsv_kraken,docker --run_bam_filtering  --bam_unmapped_type 'fastq'
+      - name: SNPCAPTURE Run the basic pipeline with the bam input profile, generating statistics with a SNP capture bed
+        run: |
+          wget https://github.com/nf-core/test-datasets/raw/eager/reference/Human/1240K.pos.list_hs37d5.0based.bed.gz && gunzip 1240K.pos.list_hs37d5.0based.bed.gz
+          nextflow run ${GITHUB_WORKSPACE} -profile test_tsv_humanbam,docker --skip_fastqc --skip_adapterremoval --skip_deduplication --snpcapture_bed 1240K.pos.list_hs37d5.0based.bed
       - name: SEXDETERMINATION Run the basic pipeline with the bam input profile, but don't convert BAM, skip everything but sex determination
         run: |
           nextflow run ${GITHUB_WORKSPACE} -profile test_tsv_humanbam,docker --skip_fastqc --skip_adapterremoval --skip_deduplication --skip_qualimap --run_sexdeterrmine

CHANGELOG.md

@@ -3,6 +3,31 @@
 The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html).
 
+## [2.4.3] - 2022-03-24
+
+### `Added`
+
+### `Fixed`
+
+- [#828](https://github.com/nf-core/eager/issues/828) Improved error message if required metagenomic screening parameters not set correctly
+- [#836](https://github.com/nf-core/eager/issues/836) Remove deprecated parameters from test profiles
+- [#838](https://github.com/nf-core/eager/issues/838) Fix --snpcapture_bed files not being picked up by Nextflow (❤ to @meganemichel for reporting)
+- [#843](https://github.com/nf-core/eager/issues/843) Re-add direct piping of AdapterRemovalFixPrefix to pigz
+- [#844](https://github.com/nf-core/eager/issues/844) Fixed reference masking prior to pmdtools
+- [#845](https://github.com/nf-core/eager/issues/845) Updates parameter documention to specify `-s` preseq parameter also applies to lc_extrap
+- [#851](https://github.com/nf-core/eager/issues/851) Fixes a file-name clash during additional_library_merge, post-BAM trimming of different UDG treated libraries of a sample
+- Renamed a range of MultiQC general stats table headers to improve clarity, documentation has been updated accordingly
+- [#857](https://github.com/nf-core/eager/issues/857) Corrected samtools fastq flag to _retain_ read-pair information when converting off-target BAM files to fastq in paired-end mapping (❤ to @alexhbnr for reporting)
+- [#866](https://github.com/nf-core/eager/issues/866) Fixed a typo in the indexing step of BWA mem when not-collapsing (❤ to @alexhbnr for reporting)
+- Corrected tutorials to reflect updated BAM trimming flags (❤ to @marcel-keller for reporting and correcting)
+
+### `Dependencies`
+
+- [#829](https://github.com/nf-core/eager/issues/829) Bumped sequencetools: 1.4.0.5 -> 1.5.2
+- Bumped MultiQC: 1.11 -> 1.12 (for run-time optimisation and tool citation information)
+
+### `Deprecated`
+
 ## [2.4.2] - 2022-01-24
 
 ### `Added`

Dockerfile

@@ -7,7 +7,7 @@ COPY environment.yml /
 RUN conda env create --quiet -f /environment.yml && conda clean -a
 
 # Add conda installation dir to PATH (instead of doing 'conda activate')
-ENV PATH /opt/conda/envs/nf-core-eager-2.4.2/bin:$PATH
+ENV PATH /opt/conda/envs/nf-core-eager-2.4.3/bin:$PATH
 
 # Dump the details of the installed packages to a file for posterity
-RUN conda env export --name nf-core-eager-2.4.2 > nf-core-eager-2.4.2.yml
+RUN conda env export --name nf-core-eager-2.4.3 > nf-core-eager-2.4.3.yml

assets/multiqc_config.yaml

@@ -61,43 +61,43 @@ extra_fn_clean_exts:
 
 top_modules:
     - 'fastqc':
-       name: 'FastQC (pre-Trimming)'
-       path_filters:
-           - '*_raw_fastqc.zip'
+        name: 'FastQC (pre-Trimming)'
+        path_filters:
+            - '*_raw_fastqc.zip'
     - 'fastp'
     - 'adapterRemoval'
     - 'fastqc':
-       name: 'FastQC (post-Trimming)'
-       path_filters:
+        name: 'FastQC (post-Trimming)'
+        path_filters:
             - '*.truncated_fastqc.zip'
             - '*.combined*_fastqc.zip'
     - 'bowtie2':
-       path_filters:
+        path_filters:
             - '*_bt2.log'
     - 'malt'
     - 'hops'
     - 'kraken'
     - 'samtools':
-       name: 'Samtools Flagstat (pre-samtools filter)'
-       path_filters:
+        name: 'Samtools Flagstat (pre-samtools filter)'
+        path_filters:
             - '*_flagstat.stats'
     - 'samtools':
-       name: 'Samtools Flagstat (post-samtools filter)'
-       path_filters:
+        name: 'Samtools Flagstat (post-samtools filter)'
+        path_filters:
             - '*_postfilterflagstat.stats'
     - 'dedup'
     - 'picard'
     - 'preseq':
-       path_filters:
-           - '*.preseq'
+        path_filters:
+            - '*.preseq'
     - 'damageprofiler'
     - 'mtnucratio'
     - 'qualimap'
     - 'sexdeterrmine'
     - 'bcftools'
     - 'multivcfanalyzer':
-       path_filters:
-           - '*MultiVCFAnalyzer.json'
+        path_filters:
+            - '*MultiVCFAnalyzer.json'
 qualimap_config:
     general_stats_coverage:
         - 1
@@ -107,7 +107,7 @@ qualimap_config:
         - 5
 
 remove_sections:
-  - sexdeterrmine-snps
+    - sexdeterrmine-snps
 
 table_columns_visible:
     FastQC (pre-Trimming):
@@ -272,5 +272,45 @@ report_section_order:
         order: -1000
     nf-core-eager-summary:
         order: -1001
-
 export_plots: true
+table_columns_name:
+    FastQC (pre-Trimming):
+        total_sequences: "Nr. Input Reads"
+        avg_sequence_length: "Length Input Reads"
+        percent_gc: "% GC Input Reads"
+        percent_duplicates: "% Dups Input Reads"
+        percent_fails: "% Failed Input Reads"
+    FastQC (post-Trimming):
+        total_sequences: "Nr. Processed Reads"
+        avg_sequence_length: "Length Processed Reads"
+        percent_gc: "% GC Processed Reads"
+        percent_duplicates: "% Dups Processed Reads"
+        percent_fails: "%Failed Processed Reads"
+    Samtools Flagstat (pre-samtools filter):
+        flagstat_total: "Nr. Reads Into Mapping"
+        mapped_passed: "Nr. Mapped Reads"
+    Samtools Flagstat (post-samtools filter):
+        flagstat_total: "Nr. Mapped Reads Post-Filter"
+        mapped_passed: "Nr. Mapped Reads Passed Post-Filter"
+    Endogenous DNA Post (%):
+        endogenous_dna_post (%): "Endogenous DNA Post-Filter (%)"
+    Picard:
+        PERCENT_DUPLICATION: "% Dup. Mapped Reads"
+    DamageProfiler:
+        mean_readlength: "Mean Length Mapped Reads"
+        median_readlength: "Median Length Mapped Reads"
+    QualiMap:
+        mapped_reads: "Nr. Dedup. Mapped Reads"
+        total_reads: "Nr. Dedup. Total Reads"
+        avg_gc: "% GC Dedup. Mapped Reads"
+    Bcftools Stats:
+        number_of_records: "Nr. Overall Variants"
+        number_of_SNPs: "Nr. SNPs"
+        number_of_indels: "Nr. InDels"
+    MALT:
+        Mappability: "% Metagenomic Mappability"
+    SexDetErrmine:
+        RateErrX: "SexDet Err X Chr"
+        RateErrY: "SexDet Err Y Chr"
+        RateX: "SexDet Rate X Chr"
+        RateY: "SexDet Rate Y Chr"

conf/test_full.config

@@ -21,7 +21,6 @@ params {
    bwaalnl = 1024
 
    run_bam_filtering = true
-   bam_discard_unmapped = true
    bam_unmapped_type = 'discard'
    bam_mapping_quality_threshold = 25
 

conf/test_stresstest_human.config

@@ -24,7 +24,6 @@ params {
    mtnucratio_header = 'ChrM'
 
    run_bam_filtering = true
-   bam_discard_unmapped = true
    bam_unmapped_type = 'discard'
    bam_mapping_quality_threshold = 30