Fixed linting issues

Author: GallVp

docs/output.md

@@ -18,7 +18,6 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
 - [GUNZIP](#gunzip) - Decompress FLNC fastas (uLTRA path only)
 - [ULTRA or MINIMAP2](#ultra-minimap2) - Map FLNCs on genome
 - [BIOPERL](#bioperl) - Remove spurious alignments (uLTRA path only, [Issue #11](https://github.com/ksahlin/ultra/issues/11))
-- [SAMTOOLS SORT](#samtools-sort) - Sort alignment and convert sam file into bam file
 - [TAMA FILE LIST](#tama-file-list) - Prepare list file for TAMA collapse
 - [TAMA COLLAPSE](#tama-collapse) - Clean gene models
 - [TAMA MERGE](#tama-merge) - Merge all annotations into one for each sample with TAMA merge
@@ -138,24 +137,12 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
 
 [BIOPERL](https://bioperl.org/) Some CIGAR string sometimes with a gap (N). This can happen when using GFF file converted to GTF file. See [Issue #11](https://github.com/ksahlin/ultra/issues/11) from uLTRA repo.
 
-### SAMTOOLS SORT
-
-<details markdown="1">
-<summary>Output files</summary>
-
-- `07_SAMTOOLS_SORT/`
-  - `<sample>.chunk<X>_sorted.bam`: The sorted aligned reads.
-
-</details>
-
-[SAMTOOLS SORT](http://www.htslib.org/doc/samtools-sort.html) sort the aligned reads and convert the sam file in bam file.
-
 ### TAMA COLLAPSE
 
 <details markdown="1">
 <summary>Output files</summary>
 
-- `08_GSTAMA_COLLAPSE/`
+- `07_GSTAMA_COLLAPSE/`
   - `<sample>.chunk<X>_collapsed.bed`: This is a bed12 format file containing the final collapsed version of your transcriptome
   - `<sample>.chunk<X>_local_density_error.txt`: This file contains the log of filtering for local density error around the splice junctions
   - `<sample>.chunk<X>_polya.txt`: This file contains the reads with potential poly A truncation
@@ -175,8 +162,9 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
 <details markdown="1">
 <summary>Output files</summary>
 
-- `09_GSTAMA_FILELIST/`
+- `08_GSTAMA_FILELIST/`
   - `<sample>.tsv`: A tsv listing bed files to merge with TAMA merge
+  - `all_samples.tsv`: A tsv listing bed files from all samples to merge with TAMA merge
 
 </details>
 
@@ -187,15 +175,15 @@ TAMA FILELIST is a home script for generating input file list for TAMA merge.
 <details markdown="1">
 <summary>Output files</summary>
 
-- `10_GSTAMA_MERGE/`
+- `09_GSTAMA_MERGE/`
   - `<sample>.bed`: This is the main merged annotation file.
   - `<sample>_gene_report.txt`: This contains a report of the genes from the merged file.
   - `<sample>_merge.txt`: This contains a bed12 format file which shows the coordinates of each input transcript matched to the merged transcript ID.
   - `<sample>_trans_report.txt`: This contains the source information for each merged transcript.
 
 </details>
 
-[TAMA MERGE](https://github.com/GenomeRIK/tama/wiki/Tama-Merge) TAMA Merge is a tool that allows you to merge multiple transcriptomes while maintaining source information.
+[TAMA MERGE](https://github.com/GenomeRIK/tama/wiki/Tama-Merge) TAMA Merge is a tool that allows you to merge multiple transcriptomes while maintaining source information. When there are two or more samples, output files corresponding to `all_samples` are also stored if `--tama_merge_all` parameter is set.
 
 ### MultiQC
 

workflows/isoseq.nf

@@ -209,6 +209,7 @@ workflow ISOSEQ {
     }
 
     if (params.aligner == "ultra") {
+        ch_versions = ch_versions.mix(GUNZIP.out.versions)
         ch_versions = ch_versions.mix(GNU_SORT.out.versions)
         ch_versions = ch_versions.mix(ULTRA_INDEX.out.versions)
         ch_versions = ch_versions.mix(ULTRA_ALIGN.out.versions)
@@ -219,6 +220,7 @@ workflow ISOSEQ {
 
     ch_versions = ch_versions.mix(GSTAMA_COLLAPSE.out.versions)
     ch_versions = ch_versions.mix(GSTAMA_MERGE.out.versions)
+    ch_versions = ch_versions.mix(GSTAMA_MERGE_ALL.out.versions)
 
     //
     // MODULE: CUSTOM_DUMPSOFTWAREVERSIONS