Update: gstama/collapse (#1057)

* 👌 IMPROVE: Add some pacbio test files

* 🐛 FIX: Add Pacbio index to test_data.config

* 👌 IMPROVE: Re add 10000 data test

* 👌 IMPROVE: Add some pbindex

* 🐛 FIX: Add pbi extension to files

* 📦 NEW: Add galgal6 chr30 test data

* 📦 NEW: Add gd-tama module

* 🐛 FIX (TEMP): Update singularity container address

* 📦 NEW: Add bamtools module

* 📦 NEW: Rewrite and rename module (gstama => gstama/collapse)

* 👌 IMPROVE: ignore test data

* 👌 IMPROVE: Remove junk files

* 👌 IMPROVE: Update output

* 👌 IMPROVE: Add channel for publishing tama's metadata outputs

* 👌 IMPROVE: Update process label

* 🐛 FIX: Use depot.galxyproject.org url for singularity

* 👌 IMPROVE: autoselect running mode

* 🐛 FIX: correct gstama collapse bash test

* 👌 IMPROVE: Update to last templates version

* 👌 IMPROVE: Update tama package and label

* 👌 IMPROVE: Final version of test datasets config

* 👌 IMPROVE: Remove useless index + Fix Typos

* 👌 IMPROVE: Update test

* 👌 IMPROVE: Add some pacbio test files

* 🐛 FIX: Add Pacbio index to test_data.config

* 👌 IMPROVE: Re add 10000 data test

* 👌 IMPROVE: Add some pbindex

* 🐛 FIX: Add pbi extension to files

* 📦 NEW: Add galgal6 chr30 test data

* 📦 NEW: Add gd-tama module

* 🐛 FIX (TEMP): Update singularity container address

* 📦 NEW: Add bamtools module

* 📦 NEW: Rewrite and rename module (gstama => gstama/collapse)

* 👌 IMPROVE: ignore test data

* 👌 IMPROVE: Update output

* 👌 IMPROVE: Add channel for publishing tama's metadata outputs

* 👌 IMPROVE: Update process label

* 🐛 FIX: Use depot.galxyproject.org url for singularity

* 👌 IMPROVE: autoselect running mode

* 🐛 FIX: correct gstama collapse bash test

* 👌 IMPROVE: Update to last templates version

* 👌 IMPROVE: Update tama package and label

* 👌 IMPROVE: Final version of test datasets config

* 👌 IMPROVE: Remove useless index + Fix Typos

* 👌 IMPROVE: Update test

* 👌 IMPROVE: delete unnecessary files

* 👌 IMPROVE: Update + clean

- Remove unnecessary files
- Update to new versions.yml file
- Better output channels

* 👌 IMPROVE: Update meta.yml and output channels

* 👌 IMPROVE: Remove useless files

* 👌 IMPROVE: Remove automatic MODE setup

* 👌 IMPROVE: Applied @jfy133 code modification suggestions

* Update modules/gstama/collapse/meta.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* 🐛 FIX: Add missing fasta option in meta.yml

* 🐛 FIX: Fix typo

* 🐛 FIX: Update package version

* Update main.nf

* Update meta.yml

* Update modules/gstama/collapse/meta.yml

* Apply suggestions from code review

* Update tests/modules/gstama/collapse/main.nf

* Update main.nf

* 👌 IMPROVE: Update to gs-tama 1.0.3

* Update modules/gstama/collapse/main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

modules/gstama/collapse/main.nf

@@ -11,11 +11,12 @@ process GSTAMA_COLLAPSE {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
-    conda (params.enable_conda ? "bioconda::gs-tama=1.0.2" : null)
+    conda (params.enable_conda ? "bioconda::gs-tama=1.0.3" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/gs-tama:1.0.2--hdfd78af_0"
+        container "https://depot.galaxyproject.org/singularity/gs-tama:1.0.3--hdfd78af_0"
     } else {
-        container "quay.io/biocontainers/gs-tama:1.0.2--hdfd78af_0"
+        container "quay.io/biocontainers/gs-tama:1.0.3--hdfd78af_0"
+
     }
 
     input:
@@ -23,7 +24,7 @@ process GSTAMA_COLLAPSE {
     path fasta
 
     output:
-    tuple val(meta), path("*.bed")                    , emit: bed
+    tuple val(meta), path("*_collapsed.bed")          , emit: bed
     tuple val(meta), path("*_trans_read.bed")         , emit: bed_trans_reads
     tuple val(meta), path("*_local_density_error.txt"), emit: local_density_error
     tuple val(meta), path("*_polya.txt")              , emit: polya

tests/modules/gstama/collapse/test.yml

@@ -4,7 +4,7 @@
     - gstama
     - gstama/collapse
   files:
-    - path: output/gstama/test_tc.bed
+    - path: output/gstama/test_tc_collapsed.bed
       md5sum: e5105198ed970a33ae0ecaa7bff421d9
     - path: output/gstama/test_tc_local_density_error.txt
       md5sum: b917ac1f14eccd590b6881a686f324d5
@@ -18,5 +18,7 @@
       md5sum: 0ca1a32f33ef05242d897d913802554b
     - path: output/gstama/test_tc_trans_report.txt
       md5sum: 33a86c15ca2acce36b2a5962f4c1adc4
+    - path: output/gstama/test_tc_varcov.txt
+      md5sum: 587fd899ff658eb66b1770a35283bfcb
     - path: output/gstama/test_tc_variants.txt
       md5sum: 5b1165e9f33faba4f7207013fc27257e