[skip ci] Changes from local review

Author: drpatelh

conf/modules.config

@@ -165,15 +165,13 @@ process {
         ext.args   = '--record-count 1000000 --seed 1'
         ext.prefix = { "${meta.id}.subsampled" }
         publishDir = [
-            mode: params.publish_dir_mode,
             enabled: false
         ]
     }
 
     withName: '.*:FASTQ_SUBSAMPLE_FQ_SALMON:SALMON_QUANT' {
         ext.args   = '--skipQuant'
         publishDir = [
-            mode: params.publish_dir_mode,
             enabled: false
         ]
     }

docs/usage.md

@@ -200,7 +200,7 @@ Notes:
 
 ### GTF filtering
 
-By default, the input GTF file will be filtered to ensure that sequence names correspond to those in the genome, and to remove rows with empty transcript identifiers. Filtering can be bypassed completely where you are confident it is not necessary, using the `--skip_gtf_filter` flag. The transcript identifer filter can be disabled specifically using `skip_gtf_transcript_filter`.
+By default, the input GTF file will be filtered to ensure that sequence names correspond to those in the genome fasta file, and to remove rows with empty transcript identifiers. Filtering can be bypassed completely where you are confident it is not necessary, using the `--skip_gtf_filter` parameter. If you just want to skip the 'transcript_id' checking component of the GTF filtering script used in the pipeline this can be disabled specifically using the `--skip_gtf_transcript_filter` parameter.
 
 ## Running the pipeline
 

modules/local/gtf_filter/main.nf

@@ -11,13 +11,13 @@ process GTF_FILTER {
     path gtf
 
     output:
-    path "*.filtered.gtf"           , emit: genome_gtf
-    path "versions.yml"              , emit: versions
+    path "*.filtered.gtf", emit: genome_gtf
+    path "versions.yml"  , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
 
-    script: // filter_gtf_for_genes_in_genome.py is bundled with the pipeline, in nf-core/rnaseq/bin/
+    script: // filter_gtf.py is bundled with the pipeline, in nf-core/rnaseq/bin/
     """
     filter_gtf.py \\
         --gtf $gtf \\

nextflow_schema.json

@@ -89,12 +89,12 @@
                     "type": "boolean",
                     "fa_icon": "fas fa-forward",
                     "description": "Skip filtering of GTF for valid scaffolds and/ or transcript IDs.",
-                    "help_text": "If you're confident on the validity of the GTF with respect to the genome file, or wish to disregard failures thriggered by the filtering module, activate this option."
+                    "help_text": "If you're confident on the validity of the GTF with respect to the genome fasta file, or wish to disregard failures thriggered by the filtering module, activate this option."
                 },
                 "skip_gtf_transcript_filter": {
                     "type": "boolean",
                     "fa_icon": "fas fa-forward",
-                    "description": "Skip just the transcript_id check of GTF filtering."
+                    "description": "Skip the 'transcript_id' checking component of the GTF filtering script used in the pipeline."
                 },
                 "gene_bed": {
                     "type": "string",

subworkflows/local/prepare_genome/main.nf

@@ -310,20 +310,20 @@ workflow PREPARE_GENOME {
     }
 
     emit:
-    fasta                   = ch_fasta                   // channel: path(genome.fasta)
-    gtf                     = ch_gtf                     // channel: path(genome.gtf)
-    filtered_gtf            = ch_filtered_gtf            // channel: path(genome.gtf)
-    fai                     = ch_fai                     // channel: path(genome.fai)
-    gene_bed                = ch_gene_bed                // channel: path(gene.bed)
-    transcript_fasta        = ch_transcript_fasta        // channel: path(transcript.fasta)
-    chrom_sizes             = ch_chrom_sizes             // channel: path(genome.sizes)
-    splicesites             = ch_splicesites             // channel: path(genome.splicesites.txt)
-    bbsplit_index           = ch_bbsplit_index           // channel: path(bbsplit/index/)
-    star_index              = ch_star_index              // channel: path(star/index/)
-    rsem_index              = ch_rsem_index              // channel: path(rsem/index/)
-    hisat2_index            = ch_hisat2_index            // channel: path(hisat2/index/)
-    salmon_index            = ch_salmon_index            // channel: path(salmon/index/)
-    kallisto_index          = ch_kallisto_index          // channel: [ meta, path(kallisto/index/) ]
+    fasta            = ch_fasta                  // channel: path(genome.fasta)
+    gtf              = ch_gtf                    // channel: path(genome.gtf)
+    filtered_gtf     = ch_filtered_gtf           // channel: path(genome.gtf)
+    fai              = ch_fai                    // channel: path(genome.fai)
+    gene_bed         = ch_gene_bed               // channel: path(gene.bed)
+    transcript_fasta = ch_transcript_fasta       // channel: path(transcript.fasta)
+    chrom_sizes      = ch_chrom_sizes            // channel: path(genome.sizes)
+    splicesites      = ch_splicesites            // channel: path(genome.splicesites.txt)
+    bbsplit_index    = ch_bbsplit_index          // channel: path(bbsplit/index/)
+    star_index       = ch_star_index             // channel: path(star/index/)
+    rsem_index       = ch_rsem_index             // channel: path(rsem/index/)
+    hisat2_index     = ch_hisat2_index           // channel: path(hisat2/index/)
+    salmon_index     = ch_salmon_index           // channel: path(salmon/index/)
+    kallisto_index   = ch_kallisto_index         // channel: [ meta, path(kallisto/index/) ]
 
-    versions                = ch_versions.ifEmpty(null)  // channel: [ versions.yml ]
+    versions         = ch_versions.ifEmpty(null) // channel: [ versions.yml ]
 }