pseudo_al -> pseudoal

Author: pinin4fjords

conf/modules.config

@@ -1085,38 +1085,38 @@ if (!params.skip_multiqc) {
 // Salmon/ Kallisto pseudoalignment options
 //
 
-if (!params.skip_pseudo_alignment && params.pseudo_aligner == 'salmon') {
+if (!params.skip_pseudoalignment && params.pseudoaligner == 'salmon') {
     process {
 
         withName: '.*:QUANTIFY_PSEUDO_ALIGNMENT:SALMON_QUANT' {
             ext.args   = { params.extra_salmon_quant_args ?: '' }
             publishDir = [
-                path: { "${params.outdir}/${params.pseudo_aligner}" },
+                path: { "${params.outdir}/${params.pseudoaligner}" },
                 mode: params.publish_dir_mode,
                 saveAs: { filename -> filename.equals('versions.yml') || filename.endsWith('_meta_info.json') ? null : filename }
             ]
         }
     }
 }
 
-if (!params.skip_pseudo_alignment && params.pseudo_aligner == 'kallisto') {
+if (!params.skip_pseudoalignment && params.pseudoaligner == 'kallisto') {
     process {
         withName: '.*:QUANTIFY_PSEUDO_ALIGNMENT:KALLISTO_QUANT' {
             ext.args = params.extra_kallisto_quant_args ?: ''
             publishDir = [
-                path: { "${params.outdir}/${params.pseudo_aligner}" },
+                path: { "${params.outdir}/${params.pseudoaligner}" },
                 mode: params.publish_dir_mode,
                 saveAs: { filename -> filename.equals('versions.yml') || filename.endsWith('.run_info.json') || filename.endsWith('.log') ? null : filename }
             ]
         }
     }
 }
 
-if (!params.skip_pseudo_alignment) {
+if (!params.skip_pseudoalignment) {
     process {
         withName: '.*:QUANTIFY_PSEUDO_ALIGNMENT:TX2GENE' {
             publishDir = [
-                path: { "${params.outdir}/${params.pseudo_aligner}" },
+                path: { "${params.outdir}/${params.pseudoaligner}" },
                 mode: params.publish_dir_mode,
                 saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
             ]
@@ -1125,15 +1125,15 @@ if (!params.skip_pseudo_alignment) {
         withName: '.*:QUANTIFY_PSEUDO_ALIGNMENT:TXIMPORT' {
             ext.prefix = { "${quant_type}.merged" }
             publishDir = [
-                path: { "${params.outdir}/${params.pseudo_aligner}" },
+                path: { "${params.outdir}/${params.pseudoaligner}" },
                 mode: params.publish_dir_mode,
                 saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
             ]
         }
 
         withName: '.*:QUANTIFY_PSEUDO_ALIGNMENT:SE_.*' {
             publishDir = [
-                path: { "${params.outdir}/${params.pseudo_aligner}" },
+                path: { "${params.outdir}/${params.pseudoaligner}" },
                 mode: params.publish_dir_mode,
                 saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
             ]
@@ -1149,9 +1149,9 @@ if (!params.skip_pseudo_alignment) {
                     "--count_col 3",
                     params.deseq2_vst ? '--vst TRUE' : ''
                 ].join(' ').trim() }
-                ext.args2  = { params.pseudo_aligner }
+                ext.args2  = { params.pseudoaligner }
                 publishDir = [
-                    path: { "${params.outdir}/${params.pseudo_aligner}/deseq2_qc" },
+                    path: { "${params.outdir}/${params.pseudoaligner}/deseq2_qc" },
                     mode: params.publish_dir_mode,
                     pattern: "*{RData,pca.vals.txt,plots.pdf,sample.dists.txt,size_factors,log}"
                 ]