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Update to topics gstama/* #11603

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0ea5e6a
Update to topics
LouisLeNezet May 11, 2026
0f80543
Fix meta
LouisLeNezet May 11, 2026
b7442ae
Merge branch 'master' into gstama
LouisLeNezet May 11, 2026
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21 changes: 12 additions & 9 deletions modules/nf-core/gstama/collapse/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -19,10 +19,9 @@ process GSTAMA_COLLAPSE {
tuple val(meta), path("*_read.txt") , emit: read
tuple val(meta), path("*_strand_check.txt") , emit: strand_check
tuple val(meta), path("*_trans_report.txt") , emit: trans_report
path "versions.yml" , emit: versions

tuple val(meta), path("*_varcov.txt") , emit: varcov , optional: true
tuple val(meta), path("*_variants.txt") , emit: variants, optional: true
tuple val("${task.process}"), val('gstama'), eval("tama_collapse.py -version | sed -n 's/tc_version_date_//p'"), emit: versions_gstama, topic: versions

when:
task.ext.when == null || task.ext.when
Expand All @@ -32,14 +31,18 @@ process GSTAMA_COLLAPSE {
def prefix = task.ext.prefix ?: "${meta.id}"
"""
tama_collapse.py \\
-s $bam \\
-f $fasta \\
-s ${bam} \\
-f ${fasta} \\
-p ${prefix} \\
$args
${args}
"""

cat <<-END_VERSIONS > versions.yml
"${task.process}":
gstama: \$( tama_collapse.py -version | grep 'tc_version_date_'|sed 's/tc_version_date_//g' )
END_VERSIONS
stub:
def prefix = task.ext.prefix ?: "${meta.id}"

"""
touch ${prefix}_{collapsed,trans_read}.bed
touch ${prefix}_{local_density_error,polya,read}.txt
touch ${prefix}_{strand_check,trans_report,varcov,variants}.txt
"""
}
86 changes: 52 additions & 34 deletions modules/nf-core/gstama/collapse/meta.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -15,7 +15,8 @@ tools:
documentation: https://github.com/GenomeRIK/tama/wiki
tool_dev_url: https://github.com/sguizard/gs-tama
doi: 10.1186/s12864-020-07123-7
licence: ["GNU GPL3"]
licence:
- "GNU GPL3"
identifier: ""
input:
- - meta:
Expand All @@ -42,8 +43,8 @@ output:
e.g. [ id:'test' ]
- "*_collapsed.bed":
type: file
description: a bed12 format file containing the final collapsed version of
your transcriptome
description: a bed12 format file containing the final collapsed version
of your transcriptome
pattern: "*.bed"
ontologies: []
bed_trans_reads:
Expand All @@ -54,16 +55,16 @@ output:
e.g. [ id:'test' ]
- "*_trans_read.bed":
type: file
description: This file uses bed12 format to show the transcript model for
each read based on the mapping prior to collapsing. This only contains the
reads which were accepted according to the defined thresholds. You can use
this file to see if there were any strange occurrences during collapsing.
It also contains the relationships between reads and collapsed transcript
models. The 1st subfield in the 4th column shows the final transcript ID
and the 2nd subfield in the 4th column shows the read ID. If you used no_cap
mode for collapsing there may be multiple lines for a single read. This
happens when a 5' degraded read can match to multiple 5' longer transcript
models.
description: This file uses bed12 format to show the transcript model
for each read based on the mapping prior to collapsing. This only
contains the reads which were accepted according to the defined
thresholds. You can use this file to see if there were any strange
occurrences during collapsing. It also contains the relationships
between reads and collapsed transcript models. The 1st subfield in the
4th column shows the final transcript ID and the 2nd subfield in the
4th column shows the read ID. If you used no_cap mode for collapsing
there may be multiple lines for a single read. This happens when a 5'
degraded read can match to multiple 5' longer transcript models.
pattern: "*_trans_read.bed"
ontologies: []
local_density_error:
Expand All @@ -74,8 +75,8 @@ output:
e.g. [ id:'test' ]
- "*_local_density_error.txt":
type: file
description: This file contains the log of filtering for local density error
around the splice junctions ("-lde")
description: This file contains the log of filtering for local density
error around the splice junctions ("-lde")
pattern: "*_local_density_error.txt"
ontologies: []
polya:
Expand All @@ -86,7 +87,8 @@ output:
e.g. [ id:'test' ]
- "*_polya.txt":
type: file
description: This file contains the reads with potential poly A truncation.
description: This file contains the reads with potential poly A
truncation.
pattern: "*_polya.txt"
ontologies: []
read:
Expand All @@ -97,9 +99,9 @@ output:
e.g. [ id:'test' ]
- "*_read.txt":
type: file
description: This file contains information for all mapped reads from the
input SAM/BAM file. It shows both accepted and discarded reads and should
match the number of mapped reads in your SAM/BAM file
description: This file contains information for all mapped reads from
the input SAM/BAM file. It shows both accepted and discarded reads and
should match the number of mapped reads in your SAM/BAM file
pattern: "*_read.txt"
ontologies: []
strand_check:
Expand All @@ -110,8 +112,8 @@ output:
e.g. [ id:'test' ]
- "*_strand_check.txt":
type: file
description: This file shows instances where the sam flag strand information
contrasted the GMAP strand information.
description: This file shows instances where the sam flag strand
information contrasted the GMAP strand information.
pattern: "*_strand_check.txt"
ontologies: []
trans_report:
Expand All @@ -122,16 +124,10 @@ output:
e.g. [ id:'test' ]
- "*_trans_report.txt":
type: file
description: This file contains collapsing information for each transcript.
description: This file contains collapsing information for each
transcript.
pattern: "*_trans_report.txt"
ontologies: []
versions:
- versions.yml:
type: file
description: File containing software versions
pattern: "versions.yml"
ontologies:
- edam: http://edamontology.org/format_3750 # YAML
varcov:
- - meta:
type: map
Expand All @@ -140,8 +136,8 @@ output:
e.g. [ id:'test' ]
- "*_varcov.txt":
type: file
description: This file contains the coverage information for each variant
detected.
description: This file contains the coverage information for each
variant detected.
pattern: "*_varcov.txt"
ontologies: []
variants:
Expand All @@ -152,11 +148,33 @@ output:
e.g. [ id:'test' ]
- "*_variants.txt":
type: file
description: This file contains the variants called. Variants are only called
if 5 or more reads show the variant at a specific locus. If you would like
to change the threshold, please make an issue about this in the Github repo.
description: This file contains the variants called. Variants are only
called if 5 or more reads show the variant at a specific locus. If you
would like to change the threshold, please make an issue about this in
the Github repo.
pattern: "*_variants.txt"
ontologies: []
versions_gstama:
- - ${task.process}:
type: string
description: The name of the process
- gstama:
type: string
description: The name of the tool
- tama_collapse.py -version | sed -n 's/tc_version_date_//p':
type: eval
description: The expression to obtain the version of the tool
topics:
versions:
- - ${task.process}:
type: string
description: The name of the process
- gstama:
type: string
description: The name of the tool
- tama_collapse.py -version | sed -n 's/tc_version_date_//p':
type: eval
description: The expression to obtain the version of the tool
authors:
- "@sguizard"
maintainers:
Expand Down
43 changes: 26 additions & 17 deletions modules/nf-core/gstama/collapse/tests/main.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -17,31 +17,40 @@ nextflow_process {
process {
"""
input[0] = [
[ id:'test' ], // meta map
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.clustered.singletons.merged.aligned.bam', checkIfExists: true)
]
input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome2.fasta', checkIfExists: true)
[ id:'test' ],
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.clustered.singletons.merged.aligned.bam', checkIfExists: true)
]
input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome2.fasta', checkIfExists: true)
"""
}
}

then {
assertAll(
{ assert process.success },
{ assert snapshot(sanitizeOutput(process.out)).match() }
)
}
}

test("test-gstama-collapse -- stub") {
options "-stub"
when {
process {
"""
input[0] = [
[ id:'test' ],
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.clustered.singletons.merged.aligned.bam', checkIfExists: true)
]
input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome2.fasta', checkIfExists: true)
"""
}
}

then {
assertAll(
{ assert process.success },
{ assert snapshot(
process.out.bed,
process.out.bed_trans_reads,
file(process.out.local_density_error[0][1]).readLines()[3..7],
file(process.out.polya[0][1]).readLines()[0],
file(process.out.read[0][1]).readLines()[3..7],
file(process.out.strand_check[0][1]).readLines()[0],
file(process.out.trans_report[0][1]).readLines()[3..7],
file(process.out.varcov[0][1]).readLines()[3..7],
file(process.out.variants[0][1]).readLines()[3..7],
process.out.versions
).match()
}
{ assert snapshot(sanitizeOutput(process.out)).match() }
)
}
}
Expand Down
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