update workflow files for new tximport script

Author: pinin4fjords

modules/local/tximport/main.nf

@@ -16,8 +16,10 @@ process TXIMPORT {
     path "*gene_counts.tsv"              , emit: counts_gene
     path "*gene_counts_length_scaled.tsv", emit: counts_gene_length_scaled
     path "*gene_counts_scaled.tsv"       , emit: counts_gene_scaled
+    path "*gene_lengths.tsv"             , emit: lengths_gene
     path "*transcript_tpm.tsv"           , emit: tpm_transcript
     path "*transcript_counts.tsv"        , emit: counts_transcript
+    path "*transcript_lengths.tsv"       , emit: lengths_transcript
     path "versions.yml"                  , emit: versions
 
     when:

subworkflows/local/quantify_pseudo/main.nf

@@ -79,12 +79,14 @@ workflow QUANTIFY_PSEUDO_ALIGNMENT {
     results                       = ch_pseudo_results                      // channel: [ val(meta), results_dir ]
     multiqc                       = ch_pseudo_multiqc                      // channel: [ val(meta), files_for_multiqc ]
 
-    tpm_gene                      = TXIMPORT.out.tpm_gene                  // channel: [ val(meta), counts ]
-    counts_gene                   = TXIMPORT.out.counts_gene               // channel: [ val(meta), counts ]
-    counts_gene_length_scaled     = TXIMPORT.out.counts_gene_length_scaled // channel: [ val(meta), counts ]
-    counts_gene_scaled            = TXIMPORT.out.counts_gene_scaled        // channel: [ val(meta), counts ]
-    tpm_transcript                = TXIMPORT.out.tpm_transcript            // channel: [ val(meta), counts ]
-    counts_transcript             = TXIMPORT.out.counts_transcript         // channel: [ val(meta), counts ]
+    tpm_gene                      = TXIMPORT.out.tpm_gene                  //    path *gene_tpm.tsv
+    counts_gene                   = TXIMPORT.out.counts_gene               //    path *gene_counts.tsv
+    lengths_gene                  = TXIMPORT.out.lengths_gene              //    path *gene_lengths.tsv
+    counts_gene_length_scaled     = TXIMPORT.out.counts_gene_length_scaled //    path *gene_counts_length_scaled.tsv
+    counts_gene_scaled            = TXIMPORT.out.counts_gene_scaled        //    path *gene_counts_scaled.tsv
+    tpm_transcript                = TXIMPORT.out.tpm_transcript            //    path *gene_tpm.tsv
+    counts_transcript             = TXIMPORT.out.counts_transcript         //    path *transcript_counts.tsv
+    lengths_transcript            = TXIMPORT.out.lengths_transript         //    path *transcript_lengths.tsv
 
     merged_gene_rds               = SE_GENE.out.rds                        //    path: *.rds
     merged_gene_rds_length_scaled = SE_GENE_LENGTH_SCALED.out.rds          //    path: *.rds

tower.yml

@@ -4,6 +4,10 @@ reports:
   "**/star_salmon/**/deseq2.plots.pdf":
     display: "All samples STAR Salmon DESeq2 QC PDF plots"
   "**/star_salmon/salmon.merged.gene_counts.tsv":
+    display: "All samples STAR Salmon mean transcript length per gene"
+  "**/star_salmon/salmon.merged.gene_lengths.tsv":
+    display: "All samples STAR Salmon transcript lengths"
+  "**/star_salmon/salmon.merged.transcript_lengths.tsv":
     display: "All samples STAR Salmon merged gene raw counts"
   "**/star_salmon/salmon.merged.gene_tpm.tsv":
     display: "All samples STAR Salmon merged gene TPM counts"
@@ -14,6 +18,10 @@ reports:
   "**/salmon/**/deseq2.plots.pdf":
     display: "All samples Salmon DESeq2 QC PDF plots"
   "**/salmon/salmon.merged.gene_counts.tsv":
+    display: "All samples Salmon mean transcript length per gene"
+  "**/salmon/salmon.merged.gene_lengths.tsv":
+    display: "All samples Salmon transcript lengths"
+  "**/salmon/salmon.merged.transcript_lengths.tsv":
     display: "All samples Salmon merged gene raw counts"
   "**/salmon/salmon.merged.gene_tpm.tsv":
     display: "All samples Salmon merged gene TPM counts"
@@ -24,6 +32,10 @@ reports:
   "**/kallisto/**/deseq2.plots.pdf":
     display: "All samples Kallisto DESeq2 QC PDF plots"
   "**/kallisto/kallisto.merged.gene_counts.tsv":
+    display: "All samples Kallisto mean transcript length per gene"
+  "**/kallisto/kallisto.merged.gene_lengths.tsv":
+    display: "All samples Kallisto transcript lengths"
+  "**/kallisto/kallisto.merged.transcript_lengths.tsv":
     display: "All samples Kallisto merged gene raw counts"
   "**/kallisto/kallisto.merged.gene_tpm.tsv":
     display: "All samples Kallisto merged gene TPM counts"