nf-core · jma1991 · Feb 21, 2023 · Feb 18, 2023
diff --git a/conf/modules.config b/conf/modules.config
@@ -226,7 +226,7 @@ if (!params.skip_alignment && (params.aligner == 'star_salmon' || params.aligner
                 '--quantMode TranscriptomeSAM',
                 '--twopassMode Basic',
                 '--outSAMtype BAM Unsorted',
-                '--readFilesCommand zcat',
+                '--readFilesCommand gunzip -c',
                 '--runRNGseed 0',
                 '--outFilterMultimapNmax 20',
                 '--alignSJDBoverhangMin 1',
@@ -453,9 +453,21 @@ if (params.pseudo_aligner == "salmon" && params.dexseq_dtu) {
 
 if (params.edger_exon) {
     process {
+        withName: 'SUBREAD_FLATTENGTF' {
+            ext.args   = [
+                "-t exon",
+                "-g ${params.gtf_group_features}",
+                '-C',
+            ].join(' ').trim()
+            publishDir = [
+                path: { "${params.outdir}/${params.aligner}/featurecounts" },
+                mode: params.publish_dir_mode,
+                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+            ]
+        }
         withName: 'SUBREAD_FEATURECOUNTS' {
             ext.args   = [
-                '-F GTF',
+                '-F SAF',
                 "-t exon",
                 "-g ${params.gtf_group_features}",
                 '-f',

diff --git a/conf/test_edger.config b/conf/test_edger.config
@@ -0,0 +1,41 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Nextflow config file for running minimal tests
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Defines input files and everything required to run a fast and simple pipeline test.
+
+    Use as follows:
+        nextflow run nf-core/rnasplice -profile test,<docker/singularity> --outdir <OUTDIR>
+
+----------------------------------------------------------------------------------------
+*/
+
+params {
+    config_profile_name        = 'Test profile'
+    config_profile_description = 'Minimal test dataset to check pipeline function'
+
+    // Limit resources so that this can run on GitHub Actions
+
+    max_cpus   = 1
+    max_memory = '6.GB'
+    max_time   = '6.h'
+
+    // Input data human chr X from hisat2 stringtie
+
+    input = 'https://raw.githubusercontent.com/nf-core/test-datasets/rnasplice/samplesheet/samplesheet.csv'
+
+    // Genome references human chr X from hisat2 stringtie
+
+    fasta = 'https://raw.githubusercontent.com/nf-core/test-datasets/rnasplice/reference/X.fa.gz'
+    gtf   = 'https://raw.githubusercontent.com/nf-core/test-datasets/rnasplice/reference/genes_chrX.gtf'
+
+    aligner = 'star'
+    pseudo_aligner = false
+    skip_alignment = false
+    rmats = false
+    dexseq_exon = false
+    edger_exon = true
+    dexseq_dtu = false
+    suppa = false
+
+}
diff --git a/modules/local/flattengtf.nf b/modules/local/flattengtf.nf
@@ -0,0 +1,30 @@
+process SUBREAD_FLATTENGTF {
+    tag "$annotation"
+    label 'process_single'
+
+    conda "bioconda::subread=2.0.1"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/subread:2.0.1--hed695b0_0' :
+        'quay.io/biocontainers/subread:2.0.1--hed695b0_0' }"
+
+    input:
+    path(annotation)
+
+    output:
+    path "annotation.saf", emit: saf
+    path "versions.yml"  , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    """
+    flattenGTF $args -a $annotation -o annotation.saf
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        subread: \$( echo \$(flattenGTF -v 2>&1) | sed -e "s/flattenGTF v//g")
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/star/align/main.nf b/modules/nf-core/star/align/main.nf
diff --git a/modules/nf-core/star/genomegenerate/main.nf b/modules/nf-core/star/genomegenerate/main.nf
diff --git a/subworkflows/local/edger_deu.nf b/subworkflows/local/edger_deu.nf
@@ -2,6 +2,7 @@
 // edgeR DEU subworkflow
 //
 
+include { SUBREAD_FLATTENGTF    } from '../../modules/local/flattengtf'
 include { SUBREAD_FEATURECOUNTS } from '../../modules/nf-core/subread/featurecounts/main'
 include { EDGER_EXON            } from '../../modules/local/edger_exon'
 
@@ -17,11 +18,16 @@ workflow EDGER_DEU {
 
     ch_versions = Channel.empty()
 
+
+    // MODULE: SUBREAD_FLATTENGTF
+
+    SUBREAD_FLATTENGTF(gtf)
+
     //
     // MODULE: SUBREAD_FEATURECOUNTS
     //
 
-    ch_feature_counts = ch_genome_bam.combine(gtf)
+    ch_feature_counts = ch_genome_bam.combine(SUBREAD_FLATTENGTF.out.saf)
 
     SUBREAD_FEATURECOUNTS(ch_feature_counts)