Bump kallistobustools to 0.28.2

modules/nf-core/kallistobustools/count/environment.yml

@@ -4,4 +4,4 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - bioconda::kb-python=0.27.2
+  - bioconda::kb-python=0.28.2

modules/nf-core/kallistobustools/count/main.nf

@@ -4,8 +4,8 @@ process KALLISTOBUSTOOLS_COUNT {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/kb-python:0.27.2--pyhdfd78af_0' :
-        'biocontainers/kb-python:0.27.2--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/kb-python:0.28.2--pyhdfd78af_2' :
+        'biocontainers/kb-python:0.28.2--pyhdfd78af_2' }"
 
     input:
     tuple val(meta), path(reads)
@@ -14,6 +14,7 @@ process KALLISTOBUSTOOLS_COUNT {
     path  t1c
     path  t2c
     val   technology
+    val   workflow_mode
 
     output:
     tuple val(meta), path ("*.count"), emit: count
@@ -27,7 +28,7 @@ process KALLISTOBUSTOOLS_COUNT {
     def args    = task.ext.args ?: ''
     def prefix  = task.ext.prefix ?: "${meta.id}"
     def cdna    = t1c ? "-c1 $t1c" : ''
-    def introns = t2c ? "-c2 $t2c" : ''
+    def intron  = t2c ? "-c2 $t2c" : ''
     def memory  = task.memory.toGiga() - 1
     """
     kb \\
@@ -36,12 +37,13 @@ process KALLISTOBUSTOOLS_COUNT {
         -i $index \\
         -g $t2g \\
         $cdna \\
-        $introns \\
+        $intron \\
         -x $technology \\
+        --workflow $workflow_mode \\
         $args \\
         -o ${prefix}.count \\
-        ${reads.join( " " )} \\
-        -m ${memory}G
+        -m ${memory}G \\
+        ${reads.join( " " )}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

modules/nf-core/kallistobustools/count/meta.yml

@@ -12,7 +12,7 @@ tools:
       homepage: https://www.kallistobus.tools/
       documentation: https://kb-python.readthedocs.io/en/latest/index.html
       tool_dev_url: https://github.com/pachterlab/kb_python
-      licence: MIT License
+      licence: ["MIT"]
 input:
   - meta:
       type: map
@@ -34,16 +34,16 @@ input:
       pattern: "*t2g.txt"
   - t1c:
       type: file
-      description: kb ref's c1 spliced_t2c file
+      description: kb ref's c1 cdna_t2c file
       pattern: "*.{cdna_t2c.txt}"
   - t2c:
       type: file
-      description: kb ref's c2 unspliced_t2c file
-      pattern: "*.{introns_t2c.txt}"
+      description: kb ref's c2 intron_t2c file
+      pattern: "*.{intron_t2c.txt}"
   - workflow_mode:
       type: string
-      description: String value defining workflow to use, can be one of "standard", "lamanno", "nucleus"
-      pattern: "{standard,lamanno,nucleus,kite}"
+      description: String value defining workflow to use, can be one of "standard", "nac", "lamanno" (obsolete)
+      pattern: "{standard,lamanno,nac}"
   - technology:
       type: string
       description: String value defining the sequencing technology used.

modules/nf-core/kallistobustools/ref/environment.yml

@@ -4,5 +4,5 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - bioconda::kb-python=0.27.2
+  - bioconda::kb-python=0.28.2
   - conda-forge::requests>=2.23.0

modules/nf-core/kallistobustools/ref/main.nf

@@ -4,8 +4,8 @@ process KALLISTOBUSTOOLS_REF {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/kb-python:0.27.2--pyhdfd78af_0' :
-        'biocontainers/kb-python:0.27.2--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/kb-python:0.28.2--pyhdfd78af_2' :
+        'biocontainers/kb-python:0.28.2--pyhdfd78af_2' }"
 
     input:
     path fasta

modules/nf-core/kallistobustools/ref/meta.yml

@@ -14,7 +14,7 @@ tools:
       documentation: https://kb-python.readthedocs.io/en/latest/index.html
       tool_dev_url: https://github.com/pachterlab/kb_python
       doi: "10.22002/D1.1876"
-      licence: MIT License
+      licence: ["MIT"]
 input:
   - fasta:
       type: file
@@ -26,8 +26,8 @@ input:
       pattern: "*.{gtf,gtf.gz}"
   - workflow_mode:
       type: string
-      description: String value defining workflow to use, can be one of "standard", "lamanno", "nucleus"
-      pattern: "{standard,lamanno,nucleus}"
+      description: String value defining workflow to use, can be one of "standard", "nac", "lamanno" (obsolete)
+      pattern: "{standard,lamanno,nac}"
 output:
   - versions:
       type: file
@@ -43,19 +43,19 @@ output:
       pattern: "*t2g.{txt}"
   - cdna:
       type: file
-      description: Cdna fasta file
+      description: cDNA fasta file
       pattern: "*cdna.{fa}"
   - intron:
       type: file
-      description: intron fasta file
+      description: Intron fasta file
       pattern: "*intron.{fa}"
   - cdna_t2c:
       type: file
-      description: cdna transcript to capture file
+      description: cDNA transcript to capture file
       pattern: "*cdna_t2c.{txt}"
   - intron_t2c:
       type: file
-      description: intron transcript to capture file
+      description: Intron transcript to capture file
       pattern: "*intron_t2c.{txt}"
 authors:
   - "@flowuenne"

tests/modules/nf-core/kallistobustools/count/main.nf

@@ -27,6 +27,7 @@ workflow test_kallistobustools_count {
       KALLISTOBUSTOOLS_REF.out.t2g, 
       KALLISTOBUSTOOLS_REF.out.cdna_t2c.ifEmpty{ [] },   // when empty the module doesn't run unless something is passed. 
       KALLISTOBUSTOOLS_REF.out.intron_t2c.ifEmpty{ [] }, // when empty the module doesn't run unless something is passed.
-      technology 
+      technology,
+      sc_workflow
     )
 }

tests/modules/nf-core/kallistobustools/count/nextflow.config

@@ -3,7 +3,7 @@ process {
     publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
 
     withName: KALLISTOBUSTOOLS_COUNT {
-        ext.args = '--cellranger -m 1 --workflow standard'
+        ext.args = '--cellranger -m 1'
     }
 
 }

tests/modules/nf-core/kallistobustools/count/test.yml

@@ -10,19 +10,21 @@
     - path: output/kallistobustools/test.count/10x_version3_whitelist.txt
       md5sum: 3d36d0a4021fd292b265e2b5e72aaaf3
     - path: output/kallistobustools/test.count/counts_unfiltered/cellranger/barcodes.tsv
-      md5sum: 2889825ad9c096ca567e057d8ddea098
+      md5sum: 001a18ffe24dcab0270ab2c1ff4f5c95
     - path: output/kallistobustools/test.count/counts_unfiltered/cellranger/genes.tsv
       md5sum: 1b31f05f9b20a4c0ac3e07b9e3ff3a14
     - path: output/kallistobustools/test.count/counts_unfiltered/cellranger/matrix.mtx
-      md5sum: b167312e8269d6bbfd609e9cdde837c7
+      md5sum: c427676ae90f740b041220e336adc5a7
     - path: output/kallistobustools/test.count/counts_unfiltered/cells_x_genes.barcodes.txt
-      md5sum: cf482bc1373075aff0fda0365dfaf3c8
+      md5sum: 41f7adaf43b60f2f4f62d6a7073688de
     - path: output/kallistobustools/test.count/counts_unfiltered/cells_x_genes.genes.txt
       md5sum: fe6d5501923867b514a0447aa4b4995f
+    - path: output/kallistobustools/test.count/counts_unfiltered/cells_x_genes.genes.names.txt
+      md5sum: b29afa75be300c7f24fbd0740a66689b
     - path: output/kallistobustools/test.count/counts_unfiltered/cells_x_genes.mtx
-      md5sum: fc1fe0cbc931e084546d8cb897e50ecc
+      md5sum: e12a45e7f7d6527f698dd9cb2e99ecd1
     - path: output/kallistobustools/test.count/inspect.json
-      md5sum: 0bfebc754e0be8aac2b50bacb52a2541
+      md5sum: bafb47a58ac1bbf9be953f21c361d266
     - path: output/kallistobustools/test.count/kb_info.json
     - path: output/kallistobustools/test.count/matrix.ec
     - path: output/kallistobustools/test.count/output.bus

tests/modules/nf-core/kallistobustools/ref/main.nf

@@ -22,11 +22,11 @@ workflow test_kallistobustools_ref_lamanno {
     KALLISTOBUSTOOLS_REF( fasta, gtf, workflow)
 }
 
-workflow test_kallistobustools_ref_nucleus {
+workflow test_kallistobustools_ref_nac {
 
     fasta       = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
     gtf         = file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)
-    workflow    = "nucleus"
+    workflow    = "nac"
 
     KALLISTOBUSTOOLS_REF( fasta, gtf, workflow)
 }

tests/modules/nf-core/kallistobustools/ref/test.yml

@@ -21,8 +21,8 @@
     - path: output/kallistobustools/kb_ref_out.idx
     - path: output/kallistobustools/t2g.txt
 
-- name: kallistobustools ref test_kallistobustools_ref_nucleus
-  command: nextflow run ./tests/modules/nf-core/kallistobustools/ref -entry test_kallistobustools_ref_nucleus -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/kallistobustools/ref/nextflow.config
+- name: kallistobustools ref test_kallistobustools_ref_nac
+  command: nextflow run ./tests/modules/nf-core/kallistobustools/ref -entry test_kallistobustools_ref_nac -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/kallistobustools/ref/nextflow.config
   tags:
     - kallistobustools/ref
     - kallistobustools