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Updated mkfastq module #5984

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merged 4 commits into from
Jul 22, 2024
Merged

Updated mkfastq module #5984

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d580457
Updated mkfastq module
Jul 16, 2024
842ae84
Combined input channels
Jul 17, 2024
e7714d7
Merge branch 'master' into master
atrigila Jul 18, 2024
06bdb36
Updated main.nf.test and snap
nschcolnicov Jul 19, 2024
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34 changes: 23 additions & 11 deletions modules/nf-core/cellranger/mkfastq/main.nf
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Original file line number Diff line number Diff line change
@@ -1,16 +1,18 @@
process CELLRANGER_MKFASTQ {
tag "mkfastq"
tag {"$meta.lane" ? "$meta.id"+"."+"$meta.lane" : "$meta.id" }
label 'process_medium'

container "nf-core/cellrangermkfastq:8.0.0"

input:
path bcl
path csv
tuple val(meta), path(csv), path(bcl)

output:
path "**/outs/fastq_path/*.fastq.gz", emit: fastq
path "versions.yml" , emit: versions
tuple val(meta), path("*_outs/outs/fastq_path/*.fastq.gz"), emit: fastq
tuple val(meta), path("*_outs/outs/fastq_path/Reports") , emit: reports
tuple val(meta), path("*_outs/outs/fastq_path/Stats") , emit: stats
tuple val(meta), path("*_outs/outs/interop_path/*.bin") , emit: interop
path "versions.yml" , emit: versions

when:
task.ext.when == null || task.ext.when
Expand All @@ -21,11 +23,11 @@ process CELLRANGER_MKFASTQ {
error "CELLRANGER_MKFASTQ module does not support Conda. Please use Docker / Singularity / Podman instead."
}
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${bcl.getSimpleName()}"
def prefix = task.ext.prefix ?: "${meta.id}" //run_dir (bcl) and id must be different because a folder is created with the id value
"""
cellranger \\
mkfastq \\
--id=${prefix} \\
--id=${prefix}_outs \\
--run=$bcl \\
--csv=$csv \\
$args
Expand All @@ -41,17 +43,27 @@ process CELLRANGER_MKFASTQ {
if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
error "CELLRANGER_MKFASTQ module does not support Conda. Please use Docker / Singularity / Podman instead."
}
def prefix = task.ext.prefix ?: "${bcl.getSimpleName()}"
def prefix = task.ext.prefix ?: "${meta.id}"
"""
mkdir -p "${prefix}/outs/fastq_path/"
mkdir -p "${prefix}_outs/outs/fastq_path/"
# data with something to avoid breaking nf-test java I/O stream
cat <<-FAKE_FQ > ${prefix}/outs/fastq_path/fake_file.fastq
cat <<-FAKE_FQ > ${prefix}_outs/outs/fastq_path/fake_file.fastq
@SEQ_ID
GATTTGGGGTTCAAAGCAGTATCGATCAAATAGTAAATCCATTTGTTCAACTCACAGTTT
+
!''*((((***+))%%%++)(%%%%).1***-+*''))**55CCF>>>>>>CCCCCCC65
FAKE_FQ
gzip -n ${prefix}/outs/fastq_path/fake_file.fastq
gzip -n ${prefix}_outs/outs/fastq_path/fake_file.fastq

# data for reports output channel
mkdir -p "${prefix}_outs/outs/fastq_path/Reports"

# data for stats output channel
mkdir -p "${prefix}_outs/outs/fastq_path/Stats"

# data for interops output channel
mkdir -p "${prefix}_outs/outs/interop_path/"
touch "${prefix}_outs/outs/interop_path/IndexMetricsOut.bin"

cat <<-END_VERSIONS > versions.yml
"${task.process}":
Expand Down
11 changes: 4 additions & 7 deletions modules/nf-core/cellranger/mkfastq/tests/main.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -18,7 +18,7 @@ nextflow_process {
process {
"""
input[0] = [
[],
[ id: 'test', lane:1 ],
file("https://cf.10xgenomics.com/supp/cell-exp/cellranger-tiny-bcl-1.2.0.tar.gz", checkIfExists: true)
]
"""
Expand All @@ -31,8 +31,7 @@ nextflow_process {
when {
process {
"""
input[0] = UNTAR.out.untar.map{ it[1] }
input[1] = file("https://cf.10xgenomics.com/supp/cell-exp/cellranger-tiny-bcl-simple-1.2.0.csv", checkIfExists: true)
input[0] = UNTAR.out.untar.map{ it -> [ [ id: 'test', lane:1 ], file("https://cf.10xgenomics.com/supp/cell-exp/cellranger-tiny-bcl-simple-1.2.0.csv", checkIfExists: true), it[1] ] }
"""
}
}
Expand All @@ -51,8 +50,7 @@ nextflow_process {
when {
process {
"""
input[0] = UNTAR.out.untar.map{ it[1] }
input[1] = file("https://cf.10xgenomics.com/supp/cell-exp/cellranger-tiny-bcl-samplesheet-1.2.0.csv", checkIfExists: true)
input[0] = UNTAR.out.untar.map{ it -> [ [ id: 'test', lane:1 ], file("https://cf.10xgenomics.com/supp/cell-exp/cellranger-tiny-bcl-samplesheet-1.2.0.csv", checkIfExists: true), it[1] ] }
"""
}
}
Expand All @@ -73,8 +71,7 @@ nextflow_process {
when {
process {
"""
input[0] = UNTAR.out.untar.map{ it[1] }
input[1] = file("https://cf.10xgenomics.com/supp/cell-exp/cellranger-tiny-bcl-simple-1.2.0.csv", checkIfExists: true)
input[0] = UNTAR.out.untar.map{ it -> [ [ id: 'test', lane:1 ], file("https://cf.10xgenomics.com/supp/cell-exp/cellranger-tiny-bcl-simple-1.2.0.csv", checkIfExists: true), it[1] ] }
"""
}
}
Expand Down
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