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Merged
nikhil merged 5 commits into from
May 8, 2026
Merged

Switch from Channel to channel #245

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cd48156
Switch from Channel to channel
nikhil May 8, 2026
4d8142b
Merge branch 'develop' into feature/update_nextflow_syntax
nikhil May 8, 2026
8ac0aa4
Remove salmon tests from conda
nikhil May 8, 2026
1d571ac
Remove artifact file
nikhil May 8, 2026
92a2c33
Merge branch 'feature/update_nextflow_syntax' of github.com:mskcc-omi…
nikhil May 8, 2026
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2 changes: 2 additions & 0 deletions .github/skip_nf_test.json
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Original file line number Diff line number Diff line change
Expand Up @@ -17,6 +17,8 @@
"modules/msk/snppileup",
"modules/msk/netmhcstabpan",
"modules/msk/genomenexus/annotationpipeline",
"modules/msk/salmon/index",
"modules/msk/salmon/quant",
"modules/msk/genomenexus/vcf2maf",
"modules/msk/rediscoverte",
"modules/msk/netmhcpan4",
Expand Down
239 changes: 0 additions & 239 deletions .github/workflows/pytest-workflow.yml
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This file was deleted.

2 changes: 1 addition & 1 deletion modules/msk/netmhc3/meta.yml
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Expand Up @@ -43,7 +43,7 @@ input:
type: string
description:
Allows netmhc to run in parallel. Should be 'MUT' or 'WT', it
will kick off two jobs. make a Channel.Of('MUT','WT') outside the module as
will kick off two jobs. make a channel.Of('MUT','WT') outside the module as
an input. Running them in series is kicked off by putting in anything other
than MUT or WT.
pattern: "WT,MUT"
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2 changes: 1 addition & 1 deletion modules/msk/netmhcpan4/meta.yml
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Expand Up @@ -43,7 +43,7 @@ input:
type: string
description:
Allows netmhcpan to run in parallel. Should be 'MUT' or 'WT', it
will kick off two jobs. make a Channel.Of('MUT','WT') outside the module as
will kick off two jobs. make a channel.Of('MUT','WT') outside the module as
an input. Running them in series is kicked off by putting in anything other
than MUT or WT.
pattern: "WT,MUT"
Expand Down
2 changes: 1 addition & 1 deletion modules/msk/netmhcstabpan/meta.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -43,7 +43,7 @@ input:
type: string
description:
Allows netmhcstabpan to run in parallel. Should be 'MUT' or 'WT',
it will kick off two jobs. make a Channel.Of('MUT','WT') outside the module
it will kick off two jobs. make a channel.Of('MUT','WT') outside the module
as an input. Running them in series is kicked off by putting in anything other
than MUT or WT.
pattern: "WT,MUT"
Expand Down
4 changes: 2 additions & 2 deletions modules/msk/salmon/quant/tests/main.nf.test
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Expand Up @@ -26,7 +26,7 @@ nextflow_process {
when {
process {
"""
input[0] = Channel.of([
input[0] = channel.of([
[ id:'test', single_end: true ], // meta map
[ file(params.test_data_mskcc['rediscoverte']['input_R1_fq_gz'], checkIfExists: true) ]
])
Expand All @@ -53,7 +53,7 @@ nextflow_process {
when {
process {
"""
input[0] = Channel.of([
input[0] = channel.of([
[ id:'test', single_end: true ], // meta map
[ file('input_R1_fq_gz') ]
])
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2 changes: 1 addition & 1 deletion subworkflows/msk/generate_mutated_peptides/main.nf
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Expand Up @@ -15,7 +15,7 @@ workflow GENERATE_MUTATED_PEPTIDES {

main:

ch_versions = Channel.empty()
ch_versions = channel.empty()

ch_maf = ch_maf_hla_sv
.map{
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30 changes: 15 additions & 15 deletions subworkflows/msk/generate_mutated_peptides/tests/main.nf.test
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Expand Up @@ -20,25 +20,25 @@ nextflow_workflow {
workflow {
"""

input[0] = Channel.of([
input[0] = channel.of([
[ id:'test', single_end:false ], // meta map
file(params.test_data_mskcc['neoantigen']['small_test_chr2and16']['somatic_filtered_maf'], checkIfExists: true),
file(params.test_data_mskcc['neoantigen']['winners_hla_txt'], checkIfExists: true),
])

input[1] = Channel.value(
input[1] = channel.value(
file(params.test_data_mskcc['neoantigen']['small_test_chr2and16']['fa_gzip'], checkIfExists: true)
)

input[2] = Channel.value(
input[2] = channel.value(
file(params.test_data_mskcc['neoantigen']['small_test_chr2and16']['gff3'], checkIfExists: true)
)

input[3] = Channel.value(
input[3] = channel.value(
file(params.test_data_mskcc['neoantigen']['gtf'], checkIfExists: true)
)

input[4] = Channel.value(
input[4] = channel.value(
file(params.test_data_mskcc['neoantigen']['cdna'], checkIfExists: true)
)

Expand All @@ -64,26 +64,26 @@ nextflow_workflow {
when {
workflow {
"""
input[0] = Channel.of([
input[0] = channel.of([
[ id:'test', single_end:false ], // meta map
file(params.test_data_mskcc['neoantigen']['small_test_chr2and16']['somatic_filtered_maf'], checkIfExists: true),
file(params.test_data_mskcc['neoantigen']['winners_hla_txt'], checkIfExists: true),
file(params.test_data_mskcc['neoantigen']['small_test_chr2and16']['sv_filtered_bedpe'], checkIfExists: true)
])

input[1] = Channel.value(
input[1] = channel.value(
file(params.test_data_mskcc['neoantigen']['small_test_chr2and16']['fa_gzip'], checkIfExists: true)
)

input[2] = Channel.value(
input[2] = channel.value(
file(params.test_data_mskcc['neoantigen']['small_test_chr2and16']['gff3'], checkIfExists: true)
)

input[3] = Channel.value(
input[3] = channel.value(
file(params.test_data_mskcc['neoantigen']['gtf'], checkIfExists: true)
)

input[4] = Channel.value(
input[4] = channel.value(
file(params.test_data_mskcc['neoantigen']['cdna'], checkIfExists: true)
)

Expand Down Expand Up @@ -114,26 +114,26 @@ nextflow_workflow {
workflow {
"""

input[0] = Channel.of([
input[0] = channel.of([
[ id:'test', single_end:false ], // meta map
file('somatic_filtered_maf', checkIfExists: false),
file('winners_hla_txt', checkIfExists: false),
file('sv_filtered_bedpe', checkIfExists: false)
])

input[1] = Channel.value(
input[1] = channel.value(
file('fa_gzip', checkIfExists: false)
)

input[2] = Channel.value(
input[2] = channel.value(
file('gff3', checkIfExists: false)
)

input[3] = Channel.value(
input[3] = channel.value(
file('gtf', checkIfExists: false)
)

input[4] = Channel.value(
input[4] = channel.value(
file('cdna', checkIfExists: false)
)

Expand Down
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