Update module: pbccs (#1018)

* 📦 NEW: First commit of pbccs module

* 👌 IMPROVE: Remove option from command + rename output (ccs -> bam)

* 👌 IMPROVE: Move .pbi output  into report channel

* 🐛FIX: Correct code after --rq option removal from command line module

- module main.nf: Remove ramaining rq input channel
- Test main.nf: Transfert rq into addParams
- Test test.yml: Update md5sums

* 🐛FIX: Repair additionnal option usage

* 👌 IMPROVE: Add some pacbio test files

* 🐛 FIX: Add Pacbio index to test_data.config

* 👌 IMPROVE: CCS is run in parallel with --chunk option

* 👌 IMPROVE: Add Pbindex in bam ouput channel

* 👌 IMPROVE: Change label to process_low

* 👌 IMPROVE: Define reports files names + add json version of txt report

* 🐛 FIX: Add missing backslashes

* 🐛 FIX: Add missing gz extension

* 🐛 FIX: update ouput channel

* 🐛 FIX: output file name

* 👌 IMPROVE: .gitignore

* 👌 IMPROVE: Update function.nf to last version

* 👌 IMPROVE: Update saveAs in main.nf

* 👌 IMPROVE: Add pbccs module

* 🐛 FIX: Fix Broken test

* 👌 IMPROVE: Update test_data.config

* 🐛 FIX: Fix test

* 👌 IMPROVE: Update path of test dataset files

* 👌 IMPROVE: Remove useless index + Fix Typos

* 📦 NEW: First commit of pbccs module

* 👌 IMPROVE: Remove option from command + rename output (ccs -> bam)

* 👌 IMPROVE: Move .pbi output  into report channel

* 🐛FIX: Correct code after --rq option removal from command line module

- module main.nf: Remove ramaining rq input channel
- Test main.nf: Transfert rq into addParams
- Test test.yml: Update md5sums

* 🐛FIX: Repair additionnal option usage

* 👌 IMPROVE: Add some pacbio test files

* 🐛 FIX: Add Pacbio index to test_data.config

* 👌 IMPROVE: CCS is run in parallel with --chunk option

* 👌 IMPROVE: Add Pbindex in bam ouput channel

* 👌 IMPROVE: Change label to process_low

* 👌 IMPROVE: Define reports files names + add json version of txt report

* 🐛 FIX: Add missing backslashes

* 🐛 FIX: Add missing gz extension

* 🐛 FIX: update ouput channel

* 🐛 FIX: output file name

* 👌 IMPROVE: .gitignore

* 👌 IMPROVE: Update function.nf to last version

* 👌 IMPROVE: Update saveAs in main.nf

* 👌 IMPROVE: Add pbccs module

* 🐛 FIX: Fix Broken test

* 👌 IMPROVE: Update test_data.config

* 🐛 FIX: Fix test

* 👌 IMPROVE: Update path of test dataset files

* 👌 IMPROVE: Remove useless index + Fix Typos

* 🐛 FIX: fill contains args

* 👌 IMPROVE: One output => One Channel

* 👌 IMPROVE: One input => One channel

* 🐛 FIX: Update tests

* 🐛 FIX: Remove TODOs from test.yaml

* 👌 IMPROVE: Revert and keep bam and pbi together

* 🐛 FIX: Remove old rq input from meta.yml

* 👌 IMPROVE: Update test to match input channels

* 👌 IMPROVE: use prefix for for output file name

* 👌 IMPROVE: Update to new versions.yml

* 👌 IMPROVE: Update pbccs from v6.0.0 to v6.0.2

* 👌 IMPROVE: Keep track of the former sample id in meta

* Update modules/pbccs/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* 👌 IMPROVE: remove former_id from meta

* 👌 IMPROVE: Use chunk number in output filename

* 🐛 FIX: Update meta.yml

* 🐛 FIX: Update reports filenames with chunk number.

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

modules/pbccs/main.nf

@@ -37,9 +37,9 @@ process PBCCS {
     ccs \\
         $bam \\
         ${prefix}.chunk${chunk_num}.bam \\
-        --report-file ${prefix}.report.txt \\
+        --report-file ${prefix}.chunk${chunk_num}.report.txt \\
-        --report-json ${prefix}.report.json \\
+        --report-json ${prefix}.chunk${chunk_num}.report.json \\
-        --metrics-json ${prefix}.metrics.json.gz \\
+        --metrics-json ${prefix}.chunk${chunk_num}.metrics.json.gz \\
         --chunk $chunk_num/$chunk_on \\
         -j $task.cpus \\
         $options.args

modules/pbccs/meta.yml

@@ -42,10 +42,26 @@ output:
       type: file
       description: File containing software versions
       pattern: "versions.yml"
-  - css:
+  - bam:
       type: file
-      description: Consensus sequences
+      description: CCS sequences in bam format
-      pattern: "*.ccs.bam"
+      pattern: "*.bam"
+  - pbi:
+      type: file
+      description: PacBio Index of CCS sequences
+      pattern: "*.pbi"
+  - report_txt:
+      type: file
+      description: Summary of CCS in txt format
+      pattern: ".txt"
+  - report_json:
+      type: file
+      description: Summary of CCS in txt json
+      pattern: ".json"
+  - metrics:
+      type: file
+      description: Metrics about zmws
+      pattern: "*.json.gz"
 
 authors:
   - "@sguizard"

tests/modules/pbccs/test.yml

@@ -4,12 +4,12 @@
     - pbccs
   files:
     - path: output/pbccs/alz.chunk2.bam
-      md5sum: d1a0266d5df64b74409a21981071a1c6
+      md5sum: 2b6451f2d0454eb08359cb84e2e4069c
     - path: output/pbccs/alz.chunk2.bam.pbi
-      md5sum: 582a4500ddcb3f4a24a443192620d039
+      md5sum: 3112cda9744e3facbf38245d41aaf080
-    - path: output/pbccs/alz.metrics.json.gz
+    - path: output/pbccs/alz.chunk2.metrics.json.gz
       contains: [ 'zmws' ]
-    - path: output/pbccs/alz.report.json
+    - path: output/pbccs/alz.chunk2.report.json
       contains: [ 'Created by pbcopper' ]
-    - path: output/pbccs/alz.report.txt
+    - path: output/pbccs/alz.chunk2.report.txt
       md5sum: bbc5bd7a1269345cf7a7f3d4c746024b