Bump version of kallistobustools/count (#1834)

* Bump version of kallistobustools/count

* Trying to update the entire call of kbtools for scrnaseq

* Improved tests for kallistobustools/count

* Add memory, remove workflow as this is passed as args now

* Update modules/kallistobustools/count/main.nf

Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>

* adding missing value

* workflow properly chained together

* changing --workflow to ext.args

* fix intron channel

* fixed checking whether filename is empty or not

* bump indentation

* fixed if else

* Fix linting

Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
Co-authored-by: Felipe Marques de Almeida <almeidafmarques@gmail.com>

modules/kallistobustools/count/main.nf

@@ -2,10 +2,10 @@ process KALLISTOBUSTOOLS_COUNT {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? 'bioconda::kb-python=0.26.3' : null)
+    conda (params.enable_conda ? 'bioconda::kb-python=0.27.2' : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/kb-python:0.26.3--pyhdfd78af_0' :
+        'https://depot.galaxyproject.org/singularity/kb-python:0.27.2--pyhdfd78af_0' :
-        'quay.io/biocontainers/kb-python:0.26.3--pyhdfd78af_0' }"
+        'quay.io/biocontainers/kb-python:0.27.2--pyhdfd78af_0' }"
 
     input:
     tuple val(meta), path(reads)
@@ -13,7 +13,6 @@ process KALLISTOBUSTOOLS_COUNT {
     path  t2g
     path  t1c
     path  t2c
-    val   workflow_mode
     val   technology
 
     output:
@@ -36,12 +35,11 @@ process KALLISTOBUSTOOLS_COUNT {
         -g $t2g \\
         $cdna \\
         $introns \\
-        --workflow $workflow_mode \\
         -x $technology \\
         $args \\
         -o ${prefix}.count \\
-        ${reads[0]} \\
+        ${reads.join( " " )} \\
-        ${reads[1]}
+        -m ${task.memory.toGiga()}G
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

tests/modules/kallistobustools/count/main.nf

@@ -2,23 +2,31 @@
 
 nextflow.enable.dsl = 2
 
+include { KALLISTOBUSTOOLS_REF   } from '../../../../modules/kallistobustools/ref/main.nf'
 include { KALLISTOBUSTOOLS_COUNT } from '../../../../modules/kallistobustools/count/main.nf'
 
 workflow test_kallistobustools_count {
 
     input   = [
         [id:'test'], // meta map
-        [ file(params.test_data['homo_sapiens']['illumina']['test_10x_1_fastq_gz'], checkIfExists: true),
+        [ 
+          file(params.test_data['homo_sapiens']['illumina']['test_10x_1_fastq_gz'], checkIfExists: true),
           file(params.test_data['homo_sapiens']['illumina']['test_10x_2_fastq_gz'], checkIfExists: true)
         ]
     ]
 
-    index      = file("https://github.com/FloWuenne/test-datasets/blob/scrnaseq/reference/kallistobustools/kb_ref.idx?raw=true", checkIfExists: true)
+    fasta       = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-    t2g        = file("https://raw.githubusercontent.com/FloWuenne/test-datasets/scrnaseq/reference/kallistobustools/t2g.txt", checkIfExists: true)
+    gtf         = file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)
-    t1c        = []
+    sc_workflow = "standard"
-    t2c        = []
-    workflow   = "standard"
     technology  = "10XV3"
 
-    KALLISTOBUSTOOLS_COUNT ( input, index, t2g, t1c, t2c, workflow, technology )
+    KALLISTOBUSTOOLS_REF(fasta, gtf, sc_workflow)
+    KALLISTOBUSTOOLS_COUNT ( 
+      input, 
+      KALLISTOBUSTOOLS_REF.out.index, 
+      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 
+    )
 }

tests/modules/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'
+        ext.args = '--cellranger -m 1 --workflow standard'
     }
 
 }

tests/modules/kallistobustools/count/test.yml

@@ -1,36 +1,33 @@
 - name: kallistobustools count test_kallistobustools_count
   command: nextflow run ./tests/modules/kallistobustools/count -entry test_kallistobustools_count -c ./tests/config/nextflow.config  -c ./tests/modules/kallistobustools/count/nextflow.config
   tags:
-    - kallistobustools/count
     - kallistobustools
+    - kallistobustools/count
   files:
+    - path: output/kallistobustools/cdna.fa
+    - path: output/kallistobustools/kb_ref_out.idx
+    - path: output/kallistobustools/t2g.txt
     - path: output/kallistobustools/test.count/10x_version3_whitelist.txt
       md5sum: 3d36d0a4021fd292b265e2b5e72aaaf3
     - path: output/kallistobustools/test.count/counts_unfiltered/cellranger/barcodes.tsv
-      md5sum: 8f734732c46f52c4d1c025bfe4134bd2
+      md5sum: 8a41142de30df61fbb9551b29dd05a83
     - path: output/kallistobustools/test.count/counts_unfiltered/cellranger/genes.tsv
-      md5sum: fbebf995a3de568db8ac028cd0c5d993
+      md5sum: 1b31f05f9b20a4c0ac3e07b9e3ff3a14
     - path: output/kallistobustools/test.count/counts_unfiltered/cellranger/matrix.mtx
-      md5sum: 4847bae27c41961496d504bcfe9890ba
+      md5sum: 5b7bff2d19fc90168733f4ac812c7d7b
     - path: output/kallistobustools/test.count/counts_unfiltered/cells_x_genes.barcodes.txt
-      md5sum: cafdf96423987e3d9e807cdc16139541
+      md5sum: 8d7ef602416818a598f5680a707756a7
     - path: output/kallistobustools/test.count/counts_unfiltered/cells_x_genes.genes.txt
-      md5sum: 52d0627aaf0418bebe3ef75ad77da53f
+      md5sum: fe6d5501923867b514a0447aa4b4995f
     - path: output/kallistobustools/test.count/counts_unfiltered/cells_x_genes.mtx
-      md5sum: d05e1582385ba5f215fa73c470343c06
+      md5sum: 0a84dc5a7570b5821da4eef6b5769a0c
     - path: output/kallistobustools/test.count/inspect.json
-      md5sum: d3d23063f3fc07f7fbd24748aa4271a9
+      md5sum: b853330f160e06fc8af170a837384ef5
     - path: output/kallistobustools/test.count/kb_info.json
-      contains:
-        - "kallisto"
     - path: output/kallistobustools/test.count/matrix.ec
-      md5sum: cd8340e3fb78d74ad85fabdbe0a778f0
     - path: output/kallistobustools/test.count/output.bus
-      md5sum: f4702922bd0c142e34b3680c2251426a
+      md5sum: f5d8efa83f107826824292cbbdb4e37b
     - path: output/kallistobustools/test.count/output.unfiltered.bus
-      md5sum: e38f99748e598e33fe035b89e7c89fb5
+      md5sum: dcbc651dc64eb38ae14e0b90795b30d2
     - path: output/kallistobustools/test.count/run_info.json
-      contains:
-        - "n_targets"
     - path: output/kallistobustools/test.count/transcripts.txt
-      md5sum: 6d583083eaf6ca81e409332a40d2e74c