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Update nextflow.config to enable skip_run_gantt option and adjust workflow logic accordingly #95

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Merged
FloWuenne merged 3 commits into from
Jun 3, 2025
Merged

Update nextflow.config to enable skip_run_gantt option and adjust workflow logic accordingly #95

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4600077
Update nextflow.config to enable skip_run_gantt option and adjust wor…
FloWuenne Jun 3, 2025
7b294de
Updated snapshots and added tags.
FloWuenne Jun 3, 2025
998d1f1
Manually making snapshot pass.
FloWuenne Jun 3, 2025
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2 changes: 1 addition & 1 deletion nextflow.config
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Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,7 @@ params {
input = null

// General pipeline options
skip_run_gantt = false
skip_run_gantt = true

// Seqera CLI options
seqera_api_endpoint = "https://api.cloud.seqera.io"
Expand Down
5 changes: 3 additions & 2 deletions tests/main.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,7 @@ nextflow_pipeline {
tag "nf-aggregate"

test("-profile test") {

tag( "test")
when {
params {
outdir = "$outputDir"
Expand Down Expand Up @@ -34,7 +34,8 @@ nextflow_pipeline {
}
}

test("-profile test_benchmark") {
test("-profile test_benchmark") {
tag("benchmark")

when {
params {
Expand Down
33 changes: 10 additions & 23 deletions tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
@@ -1,19 +1,13 @@
{
"-profile test": {
"content": [
10,
6,
{
"PLOT_RUN_GANTT": {
"python": "3.9.19",
"pandas": "1.1.5",
"plotly_express": "0.4.1",
"click": "8.0.1"
"Workflow": {
"seqeralabs/nf-aggregate": "0.7.0"
},
"SEQERA_RUNS_DUMP": {
"seqera-cli": "0.11.2 (build 2a4e8d5)"
},
"Workflow": {
"seqeralabs/nf-aggregate": "0.7.0"
}
},
[
Expand Down Expand Up @@ -54,8 +48,6 @@
"multiqc/multiqc_plots/svg/seqera_cli_wall_time_plot.svg",
"multiqc/multiqc_report.html",
"nf-core_ampliseq",
"nf-core_ampliseq/gantt",
"nf-core_ampliseq/gantt/2lXd1j7OwZVfxh_gantt.html",
"nf-core_ampliseq/runs_dump",
"nf-core_ampliseq/runs_dump/2lXd1j7OwZVfxh",
"nf-core_ampliseq/runs_dump/2lXd1j7OwZVfxh/service-info.json",
Expand All @@ -66,9 +58,6 @@
"nf-core_ampliseq/runs_dump/2lXd1j7OwZVfxh/workflow-tasks.json",
"nf-core_ampliseq/runs_dump/2lXd1j7OwZVfxh/workflow.json",
"nf-core_rnaseq",
"nf-core_rnaseq/gantt",
"nf-core_rnaseq/gantt/4Bi5xBK6E2Nbhj_gantt.html",
"nf-core_rnaseq/gantt/4LWT4uaXDaGcDY_gantt.html",
"nf-core_rnaseq/runs_dump",
"nf-core_rnaseq/runs_dump/3iFMo0NtH1Byvy",
"nf-core_rnaseq/runs_dump/3iFMo0NtH1Byvy/service-info.json",
Expand All @@ -95,8 +84,6 @@
"nf-core_rnaseq/runs_dump/4LWT4uaXDaGcDY/workflow-tasks.json",
"nf-core_rnaseq/runs_dump/4LWT4uaXDaGcDY/workflow.json",
"nf-core_scrnaseq",
"nf-core_scrnaseq/gantt",
"nf-core_scrnaseq/gantt/38QXz4OfQDpwOV_gantt.html",
"nf-core_scrnaseq/runs_dump",
"nf-core_scrnaseq/runs_dump/38QXz4OfQDpwOV",
"nf-core_scrnaseq/runs_dump/38QXz4OfQDpwOV/service-info.json",
Expand Down Expand Up @@ -149,20 +136,20 @@
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.4"
"nextflow": "25.04.3"
},
"timestamp": "2025-05-02T03:31:32.312298"
"timestamp": "2025-06-03T20:39:31.908143839"
},
"-profile test_benchmark": {
"content": [
1,
{
"Workflow": {
"seqeralabs/nf-aggregate": "0.7.0"
},
"BENCHMARK_REPORT": {
"r": "4.4.2",
"quarto-cli": "1.5.55"
},
"Workflow": {
"seqeralabs/nf-aggregate": "0.7.0"
}
},
[
Expand All @@ -172,7 +159,7 @@
"pipeline_info/collated_software_mqc_versions.yml"
],
[

]
],
"meta": {
Expand All @@ -181,4 +168,4 @@
},
"timestamp": "2025-05-01T21:01:28.073059"
}
}
}
2 changes: 1 addition & 1 deletion workflows/nf_aggregate/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -60,7 +60,7 @@ workflow NF_AGGREGATE {
//
// MODULE: Generate Gantt chart for workflow execution
//
if(!params.skip_run_gantt){
if(!skip_run_gantt){
ch_all_runs
.filter { meta, _run_dir -> meta.fusion}
.set { ch_runs_for_gantt }
Expand Down