GET ALL THE THINGS WORKING WITH VERSIONS

lianov · Oct 1, 2021 · f85818f · f85818f
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commit f85818f
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diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -48,7 +48,6 @@ jobs:
       matrix:
         parameters:
           - "--skip_qc"
-          - "--remove_ribo_rna --skip_qualimap"
           - "--skip_trimming"
           - "--gtf false"
           - "--star_index false"

diff --git a/.nf-core.yml b/.nf-core.yml
@@ -10,11 +10,11 @@ lint:
     - modules/local/get_software_versions.nf
 update:
   nf-core/modules:
-    rseqc/bamstat: "906577873b66253b0d244871bfec2eeeaff73053"
-    rseqc/inferexperiment: "906577873b66253b0d244871bfec2eeeaff73053"
-    rseqc/innerdistance: "906577873b66253b0d244871bfec2eeeaff73053"
-    rseqc/junctionannotation: "906577873b66253b0d244871bfec2eeeaff73053"
-    rseqc/junctionsaturation: "906577873b66253b0d244871bfec2eeeaff73053"
-    rseqc/readdistribution: "906577873b66253b0d244871bfec2eeeaff73053"
-    rseqc/readduplication: "906577873b66253b0d244871bfec2eeeaff73053"
-    sortmerna: "906577873b66253b0d244871bfec2eeeaff73053"
+    rseqc/bamstat: "7b3315591a149609e27914965f858c9a7e071564"
+    rseqc/inferexperiment: "7b3315591a149609e27914965f858c9a7e071564"
+    rseqc/innerdistance: "7b3315591a149609e27914965f858c9a7e071564"
+    rseqc/junctionannotation: "7b3315591a149609e27914965f858c9a7e071564"
+    rseqc/junctionsaturation: "7b3315591a149609e27914965f858c9a7e071564"
+    rseqc/readdistribution: "7b3315591a149609e27914965f858c9a7e071564"
+    rseqc/readduplication: "7b3315591a149609e27914965f858c9a7e071564"
+    sortmerna: "7b3315591a149609e27914965f858c9a7e071564"
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -9,6 +9,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 * [[#407](https://github.com/nf-core/rnaseq/issues/407)] - Filter mouse reads from PDX samples
 * [[#690](https://github.com/nf-core/rnaseq/issues/690)] - Error with post-trimmed read 2 sample names from FastQC in MultiQC
+* [[#693](https://github.com/nf-core/rnaseq/issues/693)] - Cutadapt version missing from MultiQC report
 * [[#697](https://github.com/nf-core/rnaseq/issues/697)] - pipeline_report.{txt,html} missing from pipeline_info directory
 * Added `python3` shebang to appropriate scripts in `bin/` directory
 
@@ -25,6 +26,22 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 > **NB:** Parameter has been __added__ if just the new parameter information is present.
 > **NB:** Parameter has been __removed__ if parameter information isn't present.
 
+### Software dependencies
+
+Note, since the pipeline is now using Nextflow DSL2, each process will be run with its own [Biocontainer](https://biocontainers.pro/#/registry). This means that on occasion it is entirely possible for the pipeline to be using different versions of the same tool. However, the overall software dependency changes compared to the last release have been listed below for reference.
+
+| Dependency    | Old version | New version |
+|---------------|-------------|-------------|
+| `hisat2`      | 2.2.0       | 2.2.1       |
+| `picard`      | 2.23.9      | 2.25.7      |
+| `salmon`      | 1.4.0       | 1.5.2       |
+| `samtools`    | 1.12        | 1.13        |
+| `trim-galore` | 0.6.6       | 0.6.7       |
+
+> **NB:** Dependency has been __updated__ if both old and new version information is present.
+> **NB:** Dependency has been __added__ if just the new version information is present.
+> **NB:** Dependency has been __removed__ if version information isn't present.
+
 ## [[3.3](https://github.com/nf-core/rnaseq/releases/tag/3.3)] - 2021-07-29
 
 ### Enhancements & fixes

diff --git a/CITATIONS.md b/CITATIONS.md
@@ -10,6 +10,8 @@
 
 ## Pipeline tools
 
+* [BBMap](https://sourceforge.net/projects/bbmap/)
+
 * [BEDTools](https://pubmed.ncbi.nlm.nih.gov/20110278/)
     > Quinlan AR, Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010 Mar 15;26(6):841-2. doi: 10.1093/bioinformatics/btq033. Epub 2010 Jan 28. PubMed PMID: 20110278; PubMed Central PMCID: PMC2832824.
 

diff --git a/README.md b/README.md
@@ -93,7 +93,7 @@ The nf-core/rnaseq pipeline comes with documentation about the pipeline [usage](
 
 These scripts were originally written for use at the [National Genomics Infrastructure](https://ngisweden.scilifelab.se), part of [SciLifeLab](http://www.scilifelab.se/) in Stockholm, Sweden, by Phil Ewels ([@ewels](https://github.com/ewels)) and Rickard Hammarén ([@Hammarn](https://github.com/Hammarn)).
 
-The pipeline was re-written in Nextflow DSL2 by Harshil Patel ([@drpatelh](https://github.com/drpatelh)) from [The Bioinformatics & Biostatistics Group](https://www.crick.ac.uk/research/science-technology-platforms/bioinformatics-and-biostatistics/) at [The Francis Crick Institute](https://www.crick.ac.uk/), London.
+The pipeline was re-written in Nextflow DSL2 and is primarily maintained by Harshil Patel ([@drpatelh](https://github.com/drpatelh)) from [Seqeara Labs](https://seqera.io/), Spain.
 
 Many thanks to other who have helped out along the way too, including (but not limited to):
 [@Galithil](https://github.com/Galithil),

diff --git a/modules.json b/modules.json
@@ -4,115 +4,115 @@
     "repos": {
         "nf-core/modules": {
             "bbmap/bbsplit": {
-                "git_sha": "5b1cea7f7f38b78a8fd8e2b90b1b877bd117ed96"
+                "git_sha": "7b3315591a149609e27914965f858c9a7e071564"
             },
             "cat/fastq": {
-                "git_sha": "b932210f270a1fea1f36c181abfb064448572846"
+                "git_sha": "7b3315591a149609e27914965f858c9a7e071564"
             },
             "custom/dumpsoftwareversions": {
-                "git_sha": "22ec5c6007159d441585ef54bfa6272b6f93c78a"
+                "git_sha": "7b3315591a149609e27914965f858c9a7e071564"
             },
             "fastqc": {
-                "git_sha": "ab67a1d41b63bf52fd7c147f7f8f6e8d167590b5"
+                "git_sha": "7b3315591a149609e27914965f858c9a7e071564"
             },
             "gffread": {
-                "git_sha": "906577873b66253b0d244871bfec2eeeaff73053"
+                "git_sha": "7b3315591a149609e27914965f858c9a7e071564"
             },
             "gunzip": {
-                "git_sha": "3c5492b4a383ebd822422804d74cc9e15a747b0d"
+                "git_sha": "7b3315591a149609e27914965f858c9a7e071564"
             },
             "hisat2/align": {
-                "git_sha": "9c31cf1566fa4f8660ac3973e02fe0caebe86235"
+                "git_sha": "7b3315591a149609e27914965f858c9a7e071564"
             },
             "hisat2/build": {
-                "git_sha": "906577873b66253b0d244871bfec2eeeaff73053"
+                "git_sha": "7b3315591a149609e27914965f858c9a7e071564"
             },
             "hisat2/extractsplicesites": {
-                "git_sha": "906577873b66253b0d244871bfec2eeeaff73053"
+                "git_sha": "7b3315591a149609e27914965f858c9a7e071564"
             },
             "picard/markduplicates": {
-                "git_sha": "e971f538a99bfa190f36f9303bede205e00b90a4"
+                "git_sha": "7b3315591a149609e27914965f858c9a7e071564"
             },
             "preseq/lcextrap": {
-                "git_sha": "3c5492b4a383ebd822422804d74cc9e15a747b0d"
+                "git_sha": "7b3315591a149609e27914965f858c9a7e071564"
             },
             "qualimap/rnaseq": {
-                "git_sha": "906577873b66253b0d244871bfec2eeeaff73053"
+                "git_sha": "7b3315591a149609e27914965f858c9a7e071564"
             },
             "rsem/calculateexpression": {
-                "git_sha": "9c31cf1566fa4f8660ac3973e02fe0caebe86235"
+                "git_sha": "7b3315591a149609e27914965f858c9a7e071564"
             },
             "rsem/preparereference": {
-                "git_sha": "9c31cf1566fa4f8660ac3973e02fe0caebe86235"
+                "git_sha": "7b3315591a149609e27914965f858c9a7e071564"
             },
             "rseqc/bamstat": {
-                "git_sha": "906577873b66253b0d244871bfec2eeeaff73053"
+                "git_sha": "7b3315591a149609e27914965f858c9a7e071564"
             },
             "rseqc/inferexperiment": {
-                "git_sha": "906577873b66253b0d244871bfec2eeeaff73053"
+                "git_sha": "7b3315591a149609e27914965f858c9a7e071564"
             },
             "rseqc/innerdistance": {
-                "git_sha": "906577873b66253b0d244871bfec2eeeaff73053"
+                "git_sha": "7b3315591a149609e27914965f858c9a7e071564"
             },
             "rseqc/junctionannotation": {
-                "git_sha": "906577873b66253b0d244871bfec2eeeaff73053"
+                "git_sha": "7b3315591a149609e27914965f858c9a7e071564"
             },
             "rseqc/junctionsaturation": {
-                "git_sha": "906577873b66253b0d244871bfec2eeeaff73053"
+                "git_sha": "7b3315591a149609e27914965f858c9a7e071564"
             },
             "rseqc/readdistribution": {
-                "git_sha": "906577873b66253b0d244871bfec2eeeaff73053"
+                "git_sha": "7b3315591a149609e27914965f858c9a7e071564"
             },
             "rseqc/readduplication": {
-                "git_sha": "906577873b66253b0d244871bfec2eeeaff73053"
+                "git_sha": "7b3315591a149609e27914965f858c9a7e071564"
             },
             "salmon/index": {
-                "git_sha": "43c27792583b3db3faedf189adea48939e300cf2"
+                "git_sha": "7b3315591a149609e27914965f858c9a7e071564"
             },
             "salmon/quant": {
-                "git_sha": "43c27792583b3db3faedf189adea48939e300cf2"
+                "git_sha": "7b3315591a149609e27914965f858c9a7e071564"
             },
             "samtools/flagstat": {
-                "git_sha": "43c27792583b3db3faedf189adea48939e300cf2"
+                "git_sha": "7b3315591a149609e27914965f858c9a7e071564"
             },
             "samtools/idxstats": {
-                "git_sha": "43c27792583b3db3faedf189adea48939e300cf2"
+                "git_sha": "7b3315591a149609e27914965f858c9a7e071564"
             },
             "samtools/index": {
-                "git_sha": "43c27792583b3db3faedf189adea48939e300cf2"
+                "git_sha": "7b3315591a149609e27914965f858c9a7e071564"
             },
             "samtools/sort": {
-                "git_sha": "43c27792583b3db3faedf189adea48939e300cf2"
+                "git_sha": "7b3315591a149609e27914965f858c9a7e071564"
             },
             "samtools/stats": {
-                "git_sha": "43c27792583b3db3faedf189adea48939e300cf2"
+                "git_sha": "7b3315591a149609e27914965f858c9a7e071564"
             },
             "sortmerna": {
-                "git_sha": "906577873b66253b0d244871bfec2eeeaff73053"
+                "git_sha": "7b3315591a149609e27914965f858c9a7e071564"
             },
             "stringtie/stringtie": {
-                "git_sha": "906577873b66253b0d244871bfec2eeeaff73053"
+                "git_sha": "7b3315591a149609e27914965f858c9a7e071564"
             },
             "subread/featurecounts": {
-                "git_sha": "c3687ef54bc0f651ea332c228317baf34c643c18"
+                "git_sha": "7b3315591a149609e27914965f858c9a7e071564"
             },
             "trimgalore": {
-                "git_sha": "43c27792583b3db3faedf189adea48939e300cf2"
+                "git_sha": "7b3315591a149609e27914965f858c9a7e071564"
             },
             "ucsc/bedclip": {
-                "git_sha": "906577873b66253b0d244871bfec2eeeaff73053"
+                "git_sha": "7b3315591a149609e27914965f858c9a7e071564"
             },
             "ucsc/bedgraphtobigwig": {
-                "git_sha": "9c31cf1566fa4f8660ac3973e02fe0caebe86235"
+                "git_sha": "7b3315591a149609e27914965f858c9a7e071564"
             },
             "umitools/dedup": {
-                "git_sha": "906577873b66253b0d244871bfec2eeeaff73053"
+                "git_sha": "7b3315591a149609e27914965f858c9a7e071564"
             },
             "umitools/extract": {
-                "git_sha": "906577873b66253b0d244871bfec2eeeaff73053"
+                "git_sha": "7b3315591a149609e27914965f858c9a7e071564"
             },
             "untar": {
-                "git_sha": "3c5492b4a383ebd822422804d74cc9e15a747b0d"
+                "git_sha": "7b3315591a149609e27914965f858c9a7e071564"
             }
         }
     }

diff --git a/modules/local/bedtools_genomecov.nf b/modules/local/bedtools_genomecov.nf
@@ -24,7 +24,7 @@ process BEDTOOLS_GENOMECOV {
     output:
     tuple val(meta), path("*.forward.bedGraph"), emit: bedgraph_forward
     tuple val(meta), path("*.reverse.bedGraph"), emit: bedgraph_reverse
-    path "versions.yml"                        , emit: version
+    path "versions.yml"                        , emit: versions
 
     script:
     def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"

diff --git a/modules/local/cat_additional_fasta.nf b/modules/local/cat_additional_fasta.nf
@@ -25,7 +25,7 @@ process CAT_ADDITIONAL_FASTA {
     output:
     path "${name}.fasta", emit: fasta
     path "${name}.gtf"  , emit: gtf
-    path "versions.yml" , emit: version
+    path "versions.yml" , emit: versions
 
     script:
     def genome_name  = params.genome ? params.genome : fasta.getBaseName()

diff --git a/modules/local/deseq2_qc.nf b/modules/local/deseq2_qc.nf
@@ -34,7 +34,7 @@ process DESEQ2_QC {
     path "*sample.dists_mqc.tsv", optional:true, emit: dists_multiqc
     path "*.log"                , optional:true, emit: log
     path "size_factors"         , optional:true, emit: size_factors
-    path "versions.yml"         , emit: version
+    path "versions.yml"         , emit: versions
 
     script:
     def label_lower = params.multiqc_label.toLowerCase()

diff --git a/modules/local/dupradar.nf b/modules/local/dupradar.nf
@@ -26,7 +26,7 @@ process DUPRADAR {
     tuple val(meta), path("*.pdf")    , emit: pdf
     tuple val(meta), path("*.txt")    , emit: txt
     tuple val(meta), path("*_mqc.txt"), emit: multiqc
-    path "versions.yml"               , emit: version
+    path "versions.yml"               , emit: versions
 
     script: // This script is bundled with the pipeline, in nf-core/rnaseq/bin/
     def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"

diff --git a/modules/local/get_chrom_sizes.nf b/modules/local/get_chrom_sizes.nf
@@ -22,7 +22,7 @@ process GET_CHROM_SIZES {
     output:
     path '*.sizes'     , emit: sizes
     path '*.fai'       , emit: fai
-    path "versions.yml", emit: version
+    path "versions.yml", emit: versions
 
     script:
     """

diff --git a/modules/local/gtf2bed.nf b/modules/local/gtf2bed.nf
@@ -22,7 +22,7 @@ process GTF2BED {
 
     output:
     path '*.bed'       , emit: bed
-    path "versions.yml", emit: version
+    path "versions.yml", emit: versions
 
     script: // This script is bundled with the pipeline, in nf-core/chipseq/bin/
     """

diff --git a/modules/local/gtf_gene_filter.nf b/modules/local/gtf_gene_filter.nf
@@ -22,7 +22,7 @@ process GTF_GENE_FILTER {
 
     output:
     path "*.gtf"       , emit: gtf
-    path "versions.yml", emit: version
+    path "versions.yml", emit: versions
 
     script: // filter_gtf_for_genes_in_genome.py is bundled with the pipeline, in nf-core/rnaseq/bin/
     """

diff --git a/modules/local/multiqc.nf b/modules/local/multiqc.nf
@@ -56,7 +56,7 @@ process MULTIQC {
     path "*multiqc_report.html", emit: report
     path "*_data"              , emit: data
     path "*_plots"             , optional:true, emit: plots
-    path "versions.yml"        , emit: version
+    path "versions.yml"        , emit: versions
 
     script:
     def custom_config = params.multiqc_config ? "--config $multiqc_custom_config" : ''

diff --git a/modules/local/multiqc_custom_biotype.nf b/modules/local/multiqc_custom_biotype.nf
@@ -23,7 +23,7 @@ process MULTIQC_CUSTOM_BIOTYPE {
 
     output:
     tuple val(meta), path("*.tsv"), emit: tsv
-    path "versions.yml"           , emit: version
+    path "versions.yml"           , emit: versions
 
     script:
     def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"

diff --git a/modules/local/multiqc_custom_fail_mapped.nf b/modules/local/multiqc_custom_fail_mapped.nf
@@ -20,7 +20,7 @@ process MULTIQC_CUSTOM_FAIL_MAPPED {
 
     output:
     path "*.tsv"       , emit: tsv
-    path "versions.yml", emit: version
+    path "versions.yml", emit: versions
 
     script:
     if (fail_mapped.size() > 0) {

diff --git a/modules/local/multiqc_custom_strand_check.nf b/modules/local/multiqc_custom_strand_check.nf
@@ -20,7 +20,7 @@ process MULTIQC_CUSTOM_STRAND_CHECK {
 
     output:
     path "*.tsv"       , emit: tsv
-    path "versions.yml", emit: version
+    path "versions.yml", emit: versions
 
     script:
     if (fail_strand.size() > 0) {

diff --git a/modules/local/rsem_merge_counts.nf b/modules/local/rsem_merge_counts.nf
@@ -25,7 +25,7 @@ process RSEM_MERGE_COUNTS {
     path "rsem.merged.gene_tpm.tsv"         , emit: tpm_gene
     path "rsem.merged.transcript_counts.tsv", emit: counts_transcript
     path "rsem.merged.transcript_tpm.tsv"   , emit: tpm_transcript
-    path "versions.yml"                     , emit: version
+    path "versions.yml"                     , emit: versions
 
     script:
     """

diff --git a/modules/local/salmon_merge_counts.nf b/modules/local/salmon_merge_counts.nf
@@ -31,7 +31,7 @@ process SALMON_MERGE_COUNTS {
     path "salmon.merged.gene_counts_scaled.tsv"       , emit: counts_gene_scaled
     path "salmon.merged.transcript_counts.tsv"        , emit: counts_transcript
     path "salmon.merged.transcript_tpm.tsv"           , emit: tpm_transcript
-    path "versions.yml"                               , emit: version
+    path "versions.yml"                               , emit: versions
 
     script:
     """

diff --git a/modules/local/salmon_summarizedexperiment.nf b/modules/local/salmon_summarizedexperiment.nf
@@ -24,7 +24,7 @@ process SALMON_SUMMARIZEDEXPERIMENT {
 
     output:
     path "*.rds"       , emit: rds
-    path "versions.yml", emit: version
+    path "versions.yml", emit: versions
 
     script: // This script is bundled with the pipeline, in nf-core/rnaseq/bin/
     """

diff --git a/modules/local/salmon_tx2gene.nf b/modules/local/salmon_tx2gene.nf
@@ -23,7 +23,7 @@ process SALMON_TX2GENE {
 
     output:
     path "*.tsv"       , emit: tsv
-    path "versions.yml", emit: version
+    path "versions.yml", emit: versions
 
     script: // This script is bundled with the pipeline, in nf-core/rnaseq/bin/
     """

diff --git a/modules/local/salmon_tximport.nf b/modules/local/salmon_tximport.nf
@@ -27,7 +27,7 @@ process SALMON_TXIMPORT {
     path "*gene_counts_scaled.tsv"       , emit: counts_gene_scaled
     path "*transcript_tpm.tsv"           , emit: tpm_transcript
     path "*transcript_counts.tsv"        , emit: counts_transcript
-    path "versions.yml"                  , emit: version
+    path "versions.yml"                  , emit: versions
 
     script: // This script is bundled with the pipeline, in nf-core/rnaseq/bin/
     """

diff --git a/modules/local/samplesheet_check.nf b/modules/local/samplesheet_check.nf
@@ -21,7 +21,7 @@ process SAMPLESHEET_CHECK {
 
     output:
     path '*.csv'       , emit: csv
-    path "versions.yml", emit: version
+    path "versions.yml", emit: versions
 
     script: // This script is bundled with the pipeline, in nf-core/rnaseq/bin/
     """

diff --git a/modules/local/star_align.nf b/modules/local/star_align.nf
@@ -29,7 +29,7 @@ process STAR_ALIGN {
     tuple val(meta), path('*Log.final.out')   , emit: log_final
     tuple val(meta), path('*Log.out')         , emit: log_out
     tuple val(meta), path('*Log.progress.out'), emit: log_progress
-    path "versions.yml"                       , emit: version
+    path "versions.yml"                       , emit: versions
 
     tuple val(meta), path('*sortedByCoord.out.bam')  , optional:true, emit: bam_sorted
     tuple val(meta), path('*toTranscriptome.out.bam'), optional:true, emit: bam_transcript