Merge pull request #836 from nf-core/dev

Dev -> Master for 3.8.1 release

CHANGELOG.md

@@ -3,6 +3,10 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [[3.8.1](https://github.com/nf-core/rnaseq/releases/tag/3.8.1)] - 2022-05-27
+
+- [[#834](https://github.com/nf-core/rnaseq/issues/834)] - `nf-core download` fails with version 3.8 of the pipeline
+
 ## [[3.8](https://github.com/nf-core/rnaseq/releases/tag/3.8)] - 2022-05-25
 
 ### :warning: Major enhancements

conf/modules.config

@@ -58,7 +58,7 @@ process {
         ext.args2 = '--no-same-owner'
     }
 
-    withName: 'UNTAR_.*|STAR_GENOMEGENERATE|HISAT2_BUILD' {
+    withName: 'UNTAR_.*|STAR_GENOMEGENERATE|STAR_GENOMEGENERATE_IGENOMES|HISAT2_BUILD' {
         publishDir = [
             path: { "${params.outdir}/genome/index" },
             mode: params.publish_dir_mode,
@@ -495,7 +495,7 @@ if (!params.skip_alignment) {
 
 if (!params.skip_alignment && params.aligner == 'star_salmon') {
     process {
-        withName: '.*:ALIGN_STAR:STAR_ALIGN' {
+        withName: '.*:ALIGN_STAR:STAR_ALIGN|.*:ALIGN_STAR:STAR_ALIGN_IGENOMES' {
             ext.args   = [
                 '--quantMode TranscriptomeSAM',
                 '--twopassMode Basic',

modules.json

@@ -96,6 +96,12 @@
             "sortmerna": {
                 "git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
             },
+            "star/align": {
+                "git_sha": "fb6c7bca3d55c19a793372513395e3a567bdd7ba"
+            },
+            "star/genomegenerate": {
+                "git_sha": "fb6c7bca3d55c19a793372513395e3a567bdd7ba"
+            },
             "stringtie/stringtie": {
                 "git_sha": "6d88f2da8cc5d586456e801b535cc4213e0fa2f7"
             },

modules/local/star_align_igenomes.nf

@@ -0,0 +1,73 @@
+process STAR_ALIGN_IGENOMES {
+    tag "$meta.id"
+    label 'process_high'
+
+    conda (params.enable_conda ? "bioconda::star=2.6.1d bioconda::samtools=1.10 conda-forge::gawk=5.1.0" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:59cdd445419f14abac76b31dd0d71217994cbcc9-0' :
+        'quay.io/biocontainers/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:59cdd445419f14abac76b31dd0d71217994cbcc9-0' }"
+
+    input:
+    tuple val(meta), path(reads)
+    path index
+    path gtf
+    val star_ignore_sjdbgtf
+    val seq_platform
+    val seq_center
+
+    output:
+    tuple val(meta), path('*d.out.bam')       , emit: bam
+    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: 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
+    tuple val(meta), path('*Aligned.unsort.out.bam') , optional:true, emit: bam_unsorted
+    tuple val(meta), path('*fastq.gz')               , optional:true, emit: fastq
+    tuple val(meta), path('*.tab')                   , optional:true, emit: tab
+    tuple val(meta), path('*.out.junction')          , optional:true, emit: junction
+    tuple val(meta), path('*.out.sam')               , optional:true, emit: sam
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def ignore_gtf      = star_ignore_sjdbgtf ? '' : "--sjdbGTFfile $gtf"
+    def seq_platform    = seq_platform ? "'PL:$seq_platform'" : ""
+    def seq_center      = seq_center ? "--outSAMattrRGline ID:$prefix 'CN:$seq_center' 'SM:$prefix' $seq_platform " : "--outSAMattrRGline ID:$prefix 'SM:$prefix' $seq_platform "
+    def out_sam_type    = (args.contains('--outSAMtype')) ? '' : '--outSAMtype BAM Unsorted'
+    def mv_unsorted_bam = (args.contains('--outSAMtype BAM Unsorted SortedByCoordinate')) ? "mv ${prefix}.Aligned.out.bam ${prefix}.Aligned.unsort.out.bam" : ''
+    """
+    STAR \\
+        --genomeDir $index \\
+        --readFilesIn $reads  \\
+        --runThreadN $task.cpus \\
+        --outFileNamePrefix $prefix. \\
+        $out_sam_type \\
+        $ignore_gtf \\
+        $seq_center \\
+        $args
+
+    $mv_unsorted_bam
+
+    if [ -f ${prefix}.Unmapped.out.mate1 ]; then
+        mv ${prefix}.Unmapped.out.mate1 ${prefix}.unmapped_1.fastq
+        gzip ${prefix}.unmapped_1.fastq
+    fi
+    if [ -f ${prefix}.Unmapped.out.mate2 ]; then
+        mv ${prefix}.Unmapped.out.mate2 ${prefix}.unmapped_2.fastq
+        gzip ${prefix}.unmapped_2.fastq
+    fi
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        star: \$(STAR --version | sed -e "s/STAR_//g")
+        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
+        gawk: \$(echo \$(gawk --version 2>&1) | sed 's/^.*GNU Awk //; s/, .*\$//')
+    END_VERSIONS
+    """
+}

modules/local/star_genomegenerate_igenomes.nf

@@ -0,0 +1,68 @@
+process STAR_GENOMEGENERATE_IGENOMES {
+    tag "$fasta"
+    label 'process_high'
+
+    conda (params.enable_conda ? "bioconda::star=2.6.1d bioconda::samtools=1.10 conda-forge::gawk=5.1.0" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:59cdd445419f14abac76b31dd0d71217994cbcc9-0' :
+        'quay.io/biocontainers/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:59cdd445419f14abac76b31dd0d71217994cbcc9-0' }"
+
+    input:
+    path fasta
+    path gtf
+
+    output:
+    path "star"        , emit: index
+    path "versions.yml", emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def args_list = args.tokenize()
+    def memory = task.memory ? "--limitGenomeGenerateRAM ${task.memory.toBytes() - 100000000}" : ''
+    if (args_list.contains('--genomeSAindexNbases')) {
+        """
+        mkdir star
+        STAR \\
+            --runMode genomeGenerate \\
+            --genomeDir star/ \\
+            --genomeFastaFiles $fasta \\
+            --sjdbGTFfile $gtf \\
+            --runThreadN $task.cpus \\
+            $memory \\
+            $args
+
+        cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            star: \$(STAR --version | sed -e "s/STAR_//g")
+            samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
+            gawk: \$(echo \$(gawk --version 2>&1) | sed 's/^.*GNU Awk //; s/, .*\$//')
+        END_VERSIONS
+        """
+    } else {
+        """
+        samtools faidx $fasta
+        NUM_BASES=`gawk '{sum = sum + \$2}END{if ((log(sum)/log(2))/2 - 1 > 14) {printf "%.0f", 14} else {printf "%.0f", (log(sum)/log(2))/2 - 1}}' ${fasta}.fai`
+
+        mkdir star
+        STAR \\
+            --runMode genomeGenerate \\
+            --genomeDir star/ \\
+            --genomeFastaFiles $fasta \\
+            --sjdbGTFfile $gtf \\
+            --runThreadN $task.cpus \\
+            --genomeSAindexNbases \$NUM_BASES \\
+            $memory \\
+            $args
+
+        cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            star: \$(STAR --version | sed -e "s/STAR_//g")
+            samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
+            gawk: \$(echo \$(gawk --version 2>&1) | sed 's/^.*GNU Awk //; s/, .*\$//')
+        END_VERSIONS
+        """
+    }
+}

nextflow.config

@@ -229,7 +229,7 @@ manifest {
     description     = 'RNA sequencing analysis pipeline for gene/isoform quantification and extensive quality control.'
     mainScript      = 'main.nf'
     nextflowVersion = '!>=21.10.3'
-    version         = '3.8'
+    version         = '3.8.1'
 }
 
 // Load modules.config for DSL2 module specific options