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Merged
robert-a-forsyth merged 12 commits into from
Mar 12, 2026
Merged

initial syntax changes and bulk modules update #137

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2846eab
initial syntax changes and bulk modules update
ljwharbers Mar 11, 2026
ae09ca5
manual version bump as instructed
ljwharbers Mar 11, 2026
9e513a9
mostly channel structure changes to adhere to new module input requir…
ljwharbers Mar 11, 2026
3ee366b
added new prefix to fix same output name issue
ljwharbers Mar 11, 2026
6fcfadc
fix bam stats output channel structure
ljwharbers Mar 11, 2026
90acf33
strict syntax changes
ljwharbers Mar 11, 2026
39c5053
remove the outdirs again
ljwharbers Mar 11, 2026
699d7e9
typo
ljwharbers Mar 11, 2026
1bacb2a
linting
ljwharbers Mar 11, 2026
aa54403
final strict syntax changes
ljwharbers Mar 11, 2026
f224375
severus fix and snapshot update
ljwharbers Mar 11, 2026
678ee26
precommit
ljwharbers Mar 11, 2026
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2 changes: 1 addition & 1 deletion .nf-core.yml
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Expand Up @@ -27,7 +27,7 @@ lint:
- validation.summary.beforeText
- validation.summary.afterText
schema_params: false
nf_core_version: 3.5.1
nf_core_version: 3.5.2
repository_type: pipeline
template:
author: Jonas Demeulemeester
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1 change: 1 addition & 0 deletions conf/modules.config
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Expand Up @@ -234,6 +234,7 @@ process {
]
}
withName: '.*:BCFTOOLS_SORT' {
ext.prefix = { "${meta.id}_sorted" }
ext.arge = '--output-type z'
publishDir = [
enabled: false
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44 changes: 22 additions & 22 deletions modules.json
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Expand Up @@ -13,28 +13,28 @@
},
"bcftools/concat": {
"branch": "master",
"git_sha": "345b60fff6a192d55c2a220ae413c57f29b698b7",
"git_sha": "6383d8fe58f9498eecd5aa303e71a4a932d1e9f6",
"installed_by": ["modules", "vcf_gather_bcftools"]
},
"bcftools/merge": {
"branch": "master",
"git_sha": "f17049e03697726ace7499d2fe342f892594f6f3",
"git_sha": "3d9c2f4beaa4f62b3f006928fd9095a496d1e5a8",
"installed_by": ["modules"]
},
"bcftools/sort": {
"branch": "master",
"git_sha": "e753770db613ce014b3c4bc94f6cba443427b726",
"installed_by": ["vcf_gather_bcftools"],
"git_sha": "6383d8fe58f9498eecd5aa303e71a4a932d1e9f6",
"installed_by": ["modules", "vcf_gather_bcftools"],
"patch": "modules/nf-core/bcftools/sort/bcftools-sort.diff"
},
"ensemblvep/download": {
"branch": "master",
"git_sha": "0567eee9276d4a358e5f9f01c810a149fbd241f8",
"git_sha": "90cdd21fd96ccbdb3bc90797ca69570d18391055",
"installed_by": ["modules"]
},
"ensemblvep/vep": {
"branch": "master",
"git_sha": "48ca3de1737b0144aa9fe05bea2b681f0ae45a95",
"git_sha": "890fdcff71928fc1470d3e669d4c430c8c770297",
"installed_by": ["modules"],
"patch": "modules/nf-core/ensemblvep/vep/ensemblvep-vep.diff"
},
Expand All @@ -51,80 +51,80 @@
},
"minimap2/align": {
"branch": "master",
"git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
"git_sha": "5c9f8d5b7671237c906abadc9ff732b301ca15ca",
"installed_by": ["modules"],
"patch": "modules/nf-core/minimap2/align/minimap2-align.diff"
},
"minimap2/index": {
"branch": "master",
"git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
"git_sha": "14980f759266eec42dac401fcafeb83d6c957b41",
"installed_by": ["modules"]
},
"modkit/pileup": {
"branch": "master",
"git_sha": "e8557b97c1e0e3751c5615e1fdbc5e8671eccc76",
"git_sha": "3d81317a30d1016b533982d6b84df07713ae520a",
"installed_by": ["modules"]
},
"mosdepth": {
"branch": "master",
"git_sha": "e753770db613ce014b3c4bc94f6cba443427b726",
"git_sha": "6832b69ef7f98c54876d6436360b6b945370c615",
"installed_by": ["modules"]
},
"multiqc": {
"branch": "master",
"git_sha": "5bdb098216aaf5df9c3b6343e6204cd932503c16",
"git_sha": "2c73cc8fa92cf48de3da0b643fdf357a8a290b36",
"installed_by": ["modules"]
},
"pigz/uncompress": {
"branch": "master",
"git_sha": "e753770db613ce014b3c4bc94f6cba443427b726",
"git_sha": "f84336b7fa91a65aa61d215b8c109fbb8e4b4ac6",
"installed_by": ["modules"]
},
"samtools/cat": {
"branch": "master",
"git_sha": "c8be52dba1166c678e74cda9c3a3c221635c8bb1",
"git_sha": "f9edc59be2fe25bb6fc73ca4dfc0d28246f2a2d6",
"installed_by": ["modules"]
},
"samtools/faidx": {
"branch": "master",
"git_sha": "9a48bce39a67e2cb34b8f125fc1d50f0ad98b616",
"git_sha": "b2e78932ef01165fd85829513eaca29eff8e640a",
"installed_by": ["modules"]
},
"samtools/flagstat": {
"branch": "master",
"git_sha": "e334e12a1e985adc5ffc3fc78a68be1de711de45",
"git_sha": "1d2fbdcbca677bbe8da0f9d0d2bb7c02f2cab1c9",
"installed_by": ["bam_stats_samtools"]
},
"samtools/idxstats": {
"branch": "master",
"git_sha": "c8be52dba1166c678e74cda9c3a3c221635c8bb1",
"git_sha": "1d2fbdcbca677bbe8da0f9d0d2bb7c02f2cab1c9",
"installed_by": ["bam_stats_samtools"]
},
"samtools/index": {
"branch": "master",
"git_sha": "c8be52dba1166c678e74cda9c3a3c221635c8bb1",
"git_sha": "1d2fbdcbca677bbe8da0f9d0d2bb7c02f2cab1c9",
"installed_by": ["modules"]
},
"samtools/stats": {
"branch": "master",
"git_sha": "5cb9a8694da0a0e550921636bb60bc8c56445fd7",
"git_sha": "fe93fde0845f907fc91ad7cc7d797930408824df",
"installed_by": ["bam_stats_samtools"],
"patch": "modules/nf-core/samtools/stats/samtools-stats.diff"
},
"severus": {
"branch": "master",
"git_sha": "98a699d12b141aeb3d5da5c98ebd69a320ff350d",
"git_sha": "4dd9d8439a429c7ee566e0e2347f76ddeef27e66",
"installed_by": ["modules"],
"patch": "modules/nf-core/severus/severus.diff"
},
"untar": {
"branch": "master",
"git_sha": "00ee87ebb541af0008596400ce6d5f66d79d5408",
"git_sha": "447f7bc0fa41dfc2400c8cad4c0291880dc060cf",
"installed_by": ["modules"]
},
"unzip": {
"branch": "master",
"git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
"git_sha": "4dd9d8439a429c7ee566e0e2347f76ddeef27e66",
"installed_by": ["modules"]
},
"wget": {
Expand All @@ -138,7 +138,7 @@
"nf-core": {
"bam_stats_samtools": {
"branch": "master",
"git_sha": "0b2435805036a16dcdcf21533632d956b8273ac4",
"git_sha": "7ac6cbe7c17c2dad685da7f70496c8f48ea48687",
"installed_by": ["subworkflows"]
},
"utils_nextflow_pipeline": {
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3 changes: 0 additions & 3 deletions modules/local/clair3/main.nf
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Expand Up @@ -23,9 +23,7 @@ process CLAIR3 {
task.ext.when == null || task.ext.when

script:

def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
"""
run_clair3.sh \\
--bam_fn=$bam \\
Expand All @@ -38,7 +36,6 @@ process CLAIR3 {
"""

stub:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
"""
echo "" | gzip > ${prefix}.phased_merge_output.vcf.gz
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4 changes: 0 additions & 4 deletions modules/local/clairs/main.nf
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Expand Up @@ -21,7 +21,6 @@ process CLAIRS {

script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"

"""
/opt/bin/run_clairs \
Expand All @@ -41,9 +40,6 @@ process CLAIRS {
"""

stub:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"

"""
echo "" | gzip > snvs.vcf.gz
touch snvs.vcf.gz.tbi
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15 changes: 5 additions & 10 deletions modules/local/clairsto/main.nf
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Expand Up @@ -28,13 +28,11 @@ process CLAIRSTO {

script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def conda_prefix = workflow.containerEngine == 'singularity' ? '--conda_prefix /opt/micromamba/envs/clairs-to' : ''
def gnomad = gnomad ?: 'gnomad.r2.1.af-ge-0.001.sites.vcf.gz'
def dbSNP = dbSNP ?: 'dbsnp.b138.non-somatic.sites.vcf.gz'
def onekgenomes = onekgenomes ?: '1000g-pon.sites.vcf.gz'
def colors = colors ?: 'colors-pon.sites.vcf.gz'

def gnomad_arg = gnomad ?: 'gnomad.r2.1.af-ge-0.001.sites.vcf.gz'
def dbSNP_arg = dbSNP ?: 'dbsnp.b138.non-somatic.sites.vcf.gz'
def onekgenomes_arg = onekgenomes ?: '1000g-pon.sites.vcf.gz'
def colors_arg = colors ?: 'colors-pon.sites.vcf.gz'

"""
/opt/bin/run_clairs_to \
Expand All @@ -43,16 +41,13 @@ process CLAIRSTO {
--platform $model \\
--threads $task.cpus \\
--output_dir . \\
--panel_of_normals "${gnomad},${dbSNP},${onekgenomes},${colors}" \\
--panel_of_normals "${gnomad_arg},${dbSNP_arg},${onekgenomes_arg},${colors_arg}" \\
--panel_of_normals_require_allele_matching 'True,True,False,False' \\
$conda_prefix \\
$args \\
"""

stub:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"

"""
mkdir -p output
echo "" | gzip > snv.vcf.gz
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1 change: 0 additions & 1 deletion modules/local/cramino/main.nf
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Expand Up @@ -26,7 +26,6 @@ process CRAMINO {
"""

stub:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
"""
touch ${prefix}_cramino.txt
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1 change: 0 additions & 1 deletion modules/local/fibertoolsrs/fire/main.nf
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Expand Up @@ -31,7 +31,6 @@ process FIBERTOOLSRS_FIRE {
"""

stub:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
"""
touch ${prefix}_fire.bam
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1 change: 0 additions & 1 deletion modules/local/fibertoolsrs/nucleosomes/main.nf
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Expand Up @@ -32,7 +32,6 @@ process FIBERTOOLSRS_NUCLEOSOMES {
"""

stub:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
"""
touch ${prefix}_nuc.bam
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1 change: 0 additions & 1 deletion modules/local/fibertoolsrs/predictm6a/main.nf
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Expand Up @@ -32,7 +32,6 @@ process FIBERTOOLSRS_PREDICTM6A {
"""

stub:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"

"""
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1 change: 0 additions & 1 deletion modules/local/fibertoolsrs/qc/main.nf
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Expand Up @@ -30,7 +30,6 @@ process FIBERTOOLSRS_QC {
"""

stub:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"

"""
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7 changes: 4 additions & 3 deletions modules/local/metaextract/main.nf
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Expand Up @@ -20,9 +20,11 @@ process METAEXTRACT {
script:
def args = task.ext.args ?: ''
def ont = meta.platform == 'ont'
basecall_model = ''
kinetics = ''
"""
basecall_model=""
kinetics=""
export basecall_model="${basecall_model}"
export kinetics="${kinetics}"
if [ $ont = 'true' ]; then
basecall_model=\$(samtools view -H "${bam}" ${args} | awk -F'basecall_model=' '/basecall_model=/ {print \$2; exit}' | awk '{print \$1}' | tr -d '[:space:]')
else
Expand All @@ -32,7 +34,6 @@ process METAEXTRACT {
"""

stub:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
"""
touch ${prefix}.bam
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4 changes: 0 additions & 4 deletions modules/local/vcfsplit/main.nf
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Expand Up @@ -22,8 +22,6 @@ process VCFSPLIT {
task.ext.when == null || task.ext.when

script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
"""

bcftools view -i 'FILTER="PASS"' $indel_vcf | bgzip -c > indels_pass.vcf.gz
Expand All @@ -50,8 +48,6 @@ process VCFSPLIT {
"""

stub:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
"""
echo "" | gzip > somatic.vcf.gz
echo "" | gzip > germline.vcf.gz
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1 change: 0 additions & 1 deletion modules/local/wakhan/main.nf
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Expand Up @@ -62,7 +62,6 @@ process WAKHAN {
"""

stub:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"

"""
Expand Down
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