bentsherman · bentsherman · Apr 22, 2024
diff --git a/modules/local/bedtools_genomecov/main.nf b/modules/local/bedtools_genomecov/main.nf
@@ -7,6 +7,8 @@ process BEDTOOLS_GENOMECOV {
         'https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0' :
         'biocontainers/bedtools:2.30.0--hc088bd4_0' }"
 
+    ext args: '-split -du'
+
     input:
     tuple val(meta), path(bam)
 

diff --git a/modules/local/bedtools_genomecov/nextflow.config b/modules/local/bedtools_genomecov/nextflow.config
diff --git a/modules/local/star_align_igenomes/main.nf b/modules/local/star_align_igenomes/main.nf
@@ -7,13 +7,30 @@ process STAR_ALIGN_IGENOMES {
         'https://depot.galaxyproject.org/singularity/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:59cdd445419f14abac76b31dd0d71217994cbcc9-0' :
         'biocontainers/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:59cdd445419f14abac76b31dd0d71217994cbcc9-0' }"
 
+    ext args: { [
+        '--quantMode TranscriptomeSAM',
+        '--twopassMode Basic',
+        '--outSAMtype BAM Unsorted',
+        '--readFilesCommand zcat',
+        '--runRNGseed 0',
+        '--outFilterMultimapNmax 20',
+        '--alignSJDBoverhangMin 1',
+        '--outSAMattributes NH HI AS NM MD',
+        '--quantTranscriptomeBan Singleend',
+        '--outSAMstrandField intronMotif',
+        save_unaligned ? '--outReadsUnmapped Fastx' : '',
+        extra_args ? extra_args.split("\\s(?=--)") : ''
+    ].flatten().unique(false).join(' ').trim() }
+
     input:
     tuple val(meta), path(reads)
     tuple val(meta2), path(index)
     tuple val(meta3), path(gtf)
     val star_ignore_sjdbgtf
     val seq_platform
     val seq_center
+    val save_unaligned
+    val extra_args
 
     output:
     tuple val(meta), path('*d.out.bam')       , emit: bam

diff --git a/modules/nf-core/bbmap/bbsplit/main.nf b/modules/nf-core/bbmap/bbsplit/main.nf
diff --git a/modules/nf-core/bbmap/bbsplit/nextflow.config b/modules/nf-core/bbmap/bbsplit/nextflow.config
diff --git a/modules/nf-core/gffread/main.nf b/modules/nf-core/gffread/main.nf
diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf
diff --git a/modules/nf-core/multiqc/nextflow.config b/modules/nf-core/multiqc/nextflow.config
diff --git a/modules/nf-core/preseq/lcextrap/main.nf b/modules/nf-core/preseq/lcextrap/main.nf
diff --git a/modules/nf-core/preseq/lcextrap/nextflow.config b/modules/nf-core/preseq/lcextrap/nextflow.config
diff --git a/modules/nf-core/sortmerna/main.nf b/modules/nf-core/sortmerna/main.nf
diff --git a/modules/nf-core/sortmerna/nextflow.config b/modules/nf-core/sortmerna/nextflow.config
diff --git a/modules/nf-core/star/align/main.nf b/modules/nf-core/star/align/main.nf
diff --git a/modules/nf-core/stringtie/stringtie/main.nf b/modules/nf-core/stringtie/stringtie/main.nf
diff --git a/modules/nf-core/stringtie/stringtie/nextflow.config b/modules/nf-core/stringtie/stringtie/nextflow.config
diff --git a/modules/nf-core/subread/featurecounts/main.nf b/modules/nf-core/subread/featurecounts/main.nf
diff --git a/modules/nf-core/subread/featurecounts/nextflow.config b/modules/nf-core/subread/featurecounts/nextflow.config
diff --git a/nextflow.config b/nextflow.config
@@ -26,6 +26,8 @@ params {
     igenomes_base              = 's3://ngi-igenomes/igenomes'
     igenomes_ignore            = false
 
+    gffread_args               = '--keep-exon-attrs -F -T'
+
     // UMI handling
     with_umi                   = false
     skip_umi_extract           = false

diff --git a/subworkflows/local/align_star/main.nf b/subworkflows/local/align_star/main.nf
@@ -33,7 +33,7 @@ workflow ALIGN_STAR {
     ch_fastq          = Channel.empty()
     ch_tab            = Channel.empty()
     if (is_aws_igenome) {
-        STAR_ALIGN_IGENOMES ( reads, index, gtf, star_ignore_sjdbgtf, seq_platform, seq_center )
+        STAR_ALIGN_IGENOMES ( reads, index, gtf, star_ignore_sjdbgtf, seq_platform, seq_center, params.save_unaligned, params.extra_star_align_args )
         ch_orig_bam       = STAR_ALIGN_IGENOMES.out.bam
         ch_log_final      = STAR_ALIGN_IGENOMES.out.log_final
         ch_log_out        = STAR_ALIGN_IGENOMES.out.log_out
@@ -44,7 +44,7 @@ workflow ALIGN_STAR {
         ch_tab            = STAR_ALIGN_IGENOMES.out.tab
         ch_versions       = ch_versions.mix(STAR_ALIGN_IGENOMES.out.versions.first())
     } else {
-        STAR_ALIGN ( reads, index, gtf, star_ignore_sjdbgtf, seq_platform, seq_center )
+        STAR_ALIGN ( reads, index, gtf, star_ignore_sjdbgtf, seq_platform, seq_center, params.save_unaligned, params.extra_star_align_args )
         ch_orig_bam       = STAR_ALIGN.out.bam
         ch_log_final      = STAR_ALIGN.out.log_final
         ch_log_out        = STAR_ALIGN.out.log_out

diff --git a/subworkflows/local/align_star/nextflow.config b/subworkflows/local/align_star/nextflow.config
diff --git a/subworkflows/local/prepare_genome/main.nf b/subworkflows/local/prepare_genome/main.nf
@@ -90,7 +90,7 @@ workflow PREPARE_GENOME {
             } else {
                 ch_gff = Channel.value(file(gff))
             }
-            ch_gtf      = GFFREAD ( ch_gff ).gtf
+            ch_gtf      = GFFREAD ( ch_gff, params.gffread_args ?: '' ).gtf
             ch_versions = ch_versions.mix(GFFREAD.out.versions)
         }
 

diff --git a/subworkflows/local/prepare_genome/nextflow.config b/subworkflows/local/prepare_genome/nextflow.config
@@ -3,10 +3,6 @@ process {
         ext.args2 = '--no-same-owner'
     }
 
-    withName: 'GFFREAD' {
-        ext.args   = '--keep-exon-attrs -F -T'
-    }
-
     withName: 'SALMON_INDEX' {
         ext.args   = { [
                 params.gencode ? '--gencode' : '',

diff --git a/workflows/rnaseq/main.nf b/workflows/rnaseq/main.nf
@@ -576,7 +576,8 @@ workflow RNASEQ {
     if (!params.skip_alignment && !params.skip_stringtie) {
         STRINGTIE_STRINGTIE (
             ch_genome_bam,
-            ch_gtf
+            ch_gtf,
+            params.stringtie_ignore_gtf
         )
         ch_versions = ch_versions.mix(STRINGTIE_STRINGTIE.out.versions.first())
     }
@@ -600,7 +601,9 @@ workflow RNASEQ {
             .set { ch_featurecounts }
 
         SUBREAD_FEATURECOUNTS (
-            ch_featurecounts
+            ch_featurecounts,
+            biotype,
+            params.featurecounts_feature_type
         )
         ch_versions = ch_versions.mix(SUBREAD_FEATURECOUNTS.out.versions.first())
 
@@ -777,6 +780,7 @@ workflow RNASEQ {
             ch_multiqc_files.collect(),
             ch_multiqc_config.toList(),
             ch_multiqc_custom_config.toList(),
+            params.multiqc_title,
             ch_multiqc_logo.toList()
         )
         ch_multiqc_report = MULTIQC.out.report

diff --git a/workflows/rnaseq/nextflow.config b/workflows/rnaseq/nextflow.config
@@ -1,11 +1,3 @@
-includeConfig "../../modules/local/bedtools_genomecov/nextflow.config"
-includeConfig "../../modules/nf-core/bbmap/bbsplit/nextflow.config"
-includeConfig "../../modules/nf-core/multiqc/nextflow.config"
-includeConfig "../../modules/nf-core/preseq/lcextrap/nextflow.config"
-includeConfig "../../modules/nf-core/sortmerna/nextflow.config"
-includeConfig "../../modules/nf-core/stringtie/stringtie/nextflow.config"
-includeConfig "../../modules/nf-core/subread/featurecounts/nextflow.config"
-includeConfig "../../subworkflows/local/align_star/nextflow.config"
 includeConfig "../../subworkflows/local/quantify_rsem/nextflow.config"
 includeConfig "../../subworkflows/nf-core/bam_markduplicates_picard/nextflow.config"
 includeConfig "../../subworkflows/nf-core/fastq_align_hisat2/nextflow.config"