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Fix ci confirm pass #7186

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merged 7 commits into from
Dec 10, 2024
+46 −36
Merged

Fix ci confirm pass #7186

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20a0055
update confirm-pass jobs to correctly identify failed & cancelled
sateeshperi Dec 10, 2024
2d75d8e
touch gpu & cpu module to test
sateeshperi Dec 10, 2024
9d5b93d
Merge branch 'master' into fix-ci-confirm-pass
sateeshperi Dec 10, 2024
ee147a1
Merge branch 'master' into fix-ci-confirm-pass
sateeshperi Dec 10, 2024
f9a38d3
bump NXF VER to 24.10.2
sateeshperi Dec 10, 2024
4fe1fb3
Merge branch 'master' into fix-ci-confirm-pass
sateeshperi Dec 10, 2024
8d5cefe
Merge branch 'master' into fix-ci-confirm-pass
sateeshperi Dec 10, 2024
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11 changes: 8 additions & 3 deletions .github/workflows/gpu-tests.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -108,13 +108,18 @@ jobs:
needs: [nf-test-gpu]
if: always()
steps:
- name: All tests ok
if: ${{ success() || !contains(needs.*.result, 'failure') }}
run: exit 0
- name: One or more tests failed
if: ${{ contains(needs.*.result, 'failure') }}
run: exit 1

- name: One or more tests cancelled
if: ${{ contains(needs.*.result, 'cancelled') }}
run: exit 1

- name: All tests ok
if: ${{ contains(needs.*.result, 'success') }}
run: exit 0
Comment on lines +119 to +121
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@sateeshperi This will now pass if any test passes with a success status. That's why it negated the presence of a 'failure' status before.

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negated the presence of which failure status ?

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.* is not for any single test. It is for all members of 'needs' which has only one element here so it just stands for 'nf'test-gpu'.
Secondly, if any test fails, the fail branch will be triggered first as it is now placed above the pass branch.
I created this new confirm-pass in methylseq and we tested it quite a bit with multiple runs where tests were passing, failing, being skipped, etc.


- name: debug-print
if: always()
run: |
Expand Down
11 changes: 8 additions & 3 deletions .github/workflows/nf-test.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -110,13 +110,18 @@ jobs:
needs: [nf-test]
if: always()
steps:
- name: All tests ok
if: ${{ success() || !contains(needs.*.result, 'failure') }}
run: exit 0
- name: One or more tests failed
if: ${{ contains(needs.*.result, 'failure') }}
run: exit 1

- name: One or more tests cancelled
if: ${{ contains(needs.*.result, 'cancelled') }}
run: exit 1

- name: All tests ok
if: ${{ contains(needs.*.result, 'success') }}
run: exit 0

- name: debug-print
if: always()
run: |
Expand Down
1 change: 0 additions & 1 deletion modules/nf-core/bwameth/align/tests/main.nf.test
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Expand Up @@ -117,5 +117,4 @@ nextflow_process {
)
}
}

}
14 changes: 8 additions & 6 deletions modules/nf-core/parabricks/fq2bammeth/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -27,14 +27,15 @@ process PARABRICKS_FQ2BAMMETH {
if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
error "Parabricks module does not support Conda. Please use Docker / Singularity / Podman instead."
}
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def in_fq_command = meta.single_end ? "--in-se-fq $reads" : "--in-fq $reads"
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def in_fq_command = meta.single_end ? "--in-se-fq $reads" : "--in-fq $reads"
def known_sites_command = known_sites ? known_sites.collect{"--knownSites $it"}.join(' ') : ""
def known_sites_output = known_sites ? "--out-recal-file ${prefix}.table" : ""
def num_gpus = task.accelerator ? "--num-gpus $task.accelerator.request" : ''
def known_sites_output = known_sites ? "--out-recal-file ${prefix}.table" : ""
def num_gpus = task.accelerator ? "--num-gpus $task.accelerator.request" : ''
"""
ln -sf \$(readlink $fasta) $index/$fasta

pbrun \\
fq2bam_meth \\
--ref $index/$fasta \\
Expand All @@ -44,6 +45,7 @@ process PARABRICKS_FQ2BAMMETH {
$known_sites_output \\
$num_gpus \\
$args

cat <<-END_VERSIONS > versions.yml
"${task.process}":
pbrun: \$(echo \$(pbrun version 2>&1) | sed 's/^Please.* //' )
Expand All @@ -55,11 +57,11 @@ process PARABRICKS_FQ2BAMMETH {
if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
error "Parabricks module does not support Conda. Please use Docker / Singularity / Podman instead."
}
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
"""
touch ${prefix}.bam
touch ${prefix}.bam.bai

cat <<-END_VERSIONS > versions.yml
"${task.process}":
pbrun: \$(echo \$(pbrun version 2>&1) | sed 's/^Please.* //' )
Expand Down
9 changes: 4 additions & 5 deletions modules/nf-core/parabricks/fq2bammeth/tests/main.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -5,12 +5,12 @@ nextflow_process {
process "PARABRICKS_FQ2BAMMETH"
config "./nextflow.config"

tag "gpu"
tag "bwameth/index"
tag "modules"
tag "parabricks"
tag "parabricks/fq2bammeth"
tag "modules_nfcore"
tag "gpu"

setup {
run("BWAMETH_INDEX") {
Expand All @@ -26,8 +26,7 @@ nextflow_process {
}
}


test("SRR389222 - fastq - se") {
test("SRR389222 single-end [fastq]") {

when {
process {
Expand Down Expand Up @@ -60,7 +59,7 @@ nextflow_process {
}
}

test("SRR389222 - fastq - se - stub") {
test("SRR389222 single-end [fastq] - stub") {
options '-stub'

when {
Expand Down Expand Up @@ -90,7 +89,7 @@ nextflow_process {
}
}

test("E. coli - fastq - pe - stub") {
test("E.coli paired-end [fastq] - stub") {
options '-stub'

when {
Expand Down
32 changes: 16 additions & 16 deletions modules/nf-core/parabricks/fq2bammeth/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
{
"SRR389222 - fastq - se - stub": {
"SRR389222 single-end [fastq] - stub": {
"content": [
{
"0": [
Expand All @@ -21,13 +21,13 @@
]
],
"2": [

],
"3": [

],
"4": [

],
"5": [
"versions.yml:md5,882d996a64ad457fcaf85e3a75514baf"
Expand All @@ -51,13 +51,13 @@
]
],
"bqsr_table": [

],
"duplicate_metrics": [

],
"qc_metrics": [

],
"versions": [
"versions.yml:md5,882d996a64ad457fcaf85e3a75514baf"
Expand All @@ -70,7 +70,7 @@
},
"timestamp": "2024-11-12T11:20:10.809580487"
},
"E. coli - fastq - pe - stub": {
"E.coli paired-end [fastq] - stub": {
"content": [
{
"0": [
Expand All @@ -92,13 +92,13 @@
]
],
"2": [

],
"3": [

],
"4": [

],
"5": [
"versions.yml:md5,882d996a64ad457fcaf85e3a75514baf"
Expand All @@ -122,13 +122,13 @@
]
],
"bqsr_table": [

],
"duplicate_metrics": [

],
"qc_metrics": [

],
"versions": [
"versions.yml:md5,882d996a64ad457fcaf85e3a75514baf"
Expand All @@ -141,7 +141,7 @@
},
"timestamp": "2024-11-12T11:20:18.927598721"
},
"SRR389222 - fastq - se": {
"SRR389222 single-end [fastq]": {
"content": [
"a7f7ca7b5eb503ab58790d64a0273ed6",
[
Expand All @@ -163,4 +163,4 @@
},
"timestamp": "2024-10-26T21:29:14.709022"
}
}
}
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