Update: uLTRA (#1081)

* 👌 IMPROVE: Update .gitignore

* 📦 Add ultra module

* 👌 IMPROVE: Update test input

* 👌 IMPROVE: Update and clean code

- Update to last versions.yml file
- Update meta.yml
- Correct typos

* 👌 IMPROVE: Update output channels + Rename following subtool

* 👌 IMPROVE: Remove old ultre files

* 👌 IMPROVE: Update of pytest_modules.yml

* 👌 IMPROVE: Update test.yml

* 👌 IMPROVE: Keep md5sum as much as possible

* 👌 IMPROVE: Remove old ultra files

* 👌 IMPROVE: Update of pytest_modules.yml

* 👌 IMPROVE: Update test.yml

* 👌 IMPROVE: Keep md5sum as much as possible

* 🐛 Fix: add unsaved modifications

* 🐛 FIX: Remove one inconstant md5sum

* 🐛 FIX: Grab software name using ${getSoftwareName(task.process)}

* 🐛 FIX: Remove md5sums for pickle files (not constant).

* Update modules/ultra/pipeline/main.nf

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

* Update modules/ultra/pipeline/main.nf

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

* 👌 IMPROVE: update output directory, update meta.yml

* 👌 IMPROVE: Use modules to gunzip and sort gtf

* 🐛 FIX: Set up channel correctly

* 👌 IMPROVE: Remove pickles files and databases

Those data might be useful in a debugging purpose.

* Apply suggestions from code review

* Update main.nf

* 🐛 FIX: Update uLTRA to version 0.0.4.1 + remove $(pwd)

* 👌 IMPROVE: Sort tags in test.yml

* align order of input between main.nf and meta.yml. Add ksahlin as co-author (he did update his package to overcome the pwd-problem

* Update main.nf

* Update main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: Lasse Folkersen <lassefolkersen@gmail.com>
Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>

modules/ultra/pipeline/main.nf

@@ -11,11 +11,11 @@ process ULTRA_PIPELINE {
         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::ultra_bioinformatics=0.0.4" : null)
+    conda (params.enable_conda ? "bioconda::ultra_bioinformatics=0.0.4.1" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/ultra_bioinformatics:0.0.4--pyh5e36f6f_1"
+        container "https://depot.galaxyproject.org/singularity/ultra_bioinformatics:0.0.4.1--pyh5e36f6f_0"
     } else {
-        container "quay.io/biocontainers/ultra_bioinformatics:0.0.4--pyh5e36f6f_1"
+        container "quay.io/biocontainers/ultra_bioinformatics:0.0.4.1--pyh5e36f6f_0"
     }
 
     input:
@@ -35,9 +35,9 @@ process ULTRA_PIPELINE {
         --t $task.cpus \\
         --prefix $prefix \\
         $options.args \\
-        \$(pwd)/$genome \\
+        $genome \\
-        \$(pwd)/$gtf \\
+        $gtf \\
-        \$(pwd)/$reads \\
+        $reads \\
         ./
 
     cat <<-END_VERSIONS > versions.yml

modules/ultra/pipeline/meta.yml

@@ -18,6 +18,10 @@ input:
       description: |
         Groovy Map containing sample information
         e.g. [ id:'test', single_end:false ]
+  - reads:
+      type: file
+      description: A fasta or fastq file of reads to align
+      pattern: "*.{fasta,fastq}"
   - genome:
       type: file
       description: fasta file of reference genome
@@ -26,10 +30,6 @@ input:
       type: file
       description: A annotation of use the genome
       pattern: "*.gtf"
-  - reads:
-      type: file
-      description: A fasta or fastq file of reads to align
-      pattern: "*.{fasta,fastq}"
 
 output:
   - meta:
@@ -48,3 +48,5 @@ output:
 
 authors:
   - "@sguizard"
+  - "@lassefolkersen"
+  - "@ksahlin"

tests/modules/ultra/pipeline/main.nf

@@ -8,18 +8,15 @@ include { GFFREAD        } from '../../../../modules/gffread/main.nf'        add
 
 workflow test_ultra_pipeline {
 
-    fastq  = file(params.test_data['homo_sapiens']['pacbio']['hifi']        , checkIfExists: true)
+    input = [
+        [ id:'test', single_end:false ],
+        file(params.test_data['homo_sapiens']['pacbio']['hifi'], checkIfExists: true)
+    ]
+    GUNZIP ( input )
+
     gtf    = file(params.test_data['homo_sapiens']['genome']['genome_gtf']  , checkIfExists: true)
     genome = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-
-    GUNZIP ( fastq )
     GFFREAD ( gtf )
 
-    GUNZIP
+    ULTRA_PIPELINE ( GUNZIP.out.gunzip, genome, GFFREAD.out.gtf )
-        .out
-        .gunzip
-        .map { [ [ id:'test', single_end:false ], it ] }
-        .set { input }
-
-    ULTRA_PIPELINE ( input, genome, GFFREAD.out.gtf )
 }

tests/modules/ultra/pipeline/test.yml

@@ -1,8 +1,8 @@
 - name: ultra pipeline test_ultra_pipeline
   command: nextflow run tests/modules/ultra/pipeline -entry test_ultra_pipeline -c tests/config/nextflow.config
   tags:
-    - ultra/pipeline
     - ultra
+    - ultra/pipeline
   files:
     - path: output/gffread/genome_sorted.gtf
       md5sum: c0b034860c679a354cd093109ed90437