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Merge pull request #14 from GallVp/feat/nfcore
Added input schema and config from the nf-core template
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,11 @@ | ||
| #!/usr/bin/env bash | ||
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| set -euo pipefail | ||
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| config_version=$(sed -n "/^\s*version\s*=\s*'/s/version//p" nextflow.config | tr -d "=[:space:]'") | ||
| perl_version=$(sed -n 's|^my $version = "\(.*\)";|\1|p' EDTA.pl | tr -d '[:space:]') | ||
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| if [[ "v$config_version" != $perl_version ]]; then | ||
| echo "config_version (v$config_version) != perl_version ($perl_version)" | ||
| exit 1 | ||
| fi |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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@@ -46,7 +46,7 @@ jobs: | |
| fail-fast: false | ||
| matrix: | ||
| NXF_VER: | ||
| - "24.04.2" | ||
| - "24.10.3" | ||
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| nf_test_files: ["${{ fromJson(needs.nf-test-changes.outputs.nf_test_files) }}"] | ||
| profile: [conda, docker, singularity] | ||
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@@ -72,7 +72,7 @@ jobs: | |
| - uses: nf-core/[email protected] | ||
| with: | ||
| version: 0.9.0 | ||
| version: 0.9.2 | ||
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| - name: Setup apptainer | ||
| if: matrix.profile == 'singularity' | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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@@ -5,3 +5,4 @@ work/ | |
| .nextflow/* | ||
| results/ | ||
| .nf-test* | ||
| null/ | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,49 @@ | ||
| process { | ||
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| cpus = { 1 * task.attempt } | ||
| memory = { 6.GB * task.attempt } | ||
| time = { 4.h * task.attempt } | ||
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| errorStrategy = { task.exitStatus in ((130..145) + 104) ? 'retry' : 'finish' } | ||
| maxRetries = 1 | ||
| maxErrors = '-1' | ||
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| // Process-specific resource requirements | ||
| // NOTE - Please try and re-use the labels below as much as possible. | ||
| // These labels are used and recognised by default in DSL2 files hosted on nf-core/modules. | ||
| // If possible, it would be nice to keep the same label naming convention when | ||
| // adding in your local modules too. | ||
| withLabel:process_single { | ||
| cpus = { 1 } | ||
| memory = { 6.GB * task.attempt } | ||
| time = { 4.h * task.attempt } | ||
| } | ||
| withLabel:process_low { | ||
| cpus = { 2 * task.attempt } | ||
| memory = { 12.GB * task.attempt } | ||
| time = { 4.h * task.attempt } | ||
| } | ||
| withLabel:process_medium { | ||
| cpus = { 6 * task.attempt } | ||
| memory = { 36.GB * task.attempt } | ||
| time = { 8.h * task.attempt } | ||
| } | ||
| withLabel:process_high { | ||
| cpus = { 12 * task.attempt } | ||
| memory = { 72.GB * task.attempt } | ||
| time = { 16.h * task.attempt } | ||
| } | ||
| withLabel:process_long { | ||
| time = { 20.h * task.attempt } | ||
| } | ||
| withLabel:process_high_memory { | ||
| memory = { 200.GB * task.attempt } | ||
| } | ||
| withLabel:error_ignore { | ||
| errorStrategy = 'ignore' | ||
| } | ||
| withLabel:error_retry { | ||
| errorStrategy = 'retry' | ||
| maxRetries = 2 | ||
| } | ||
| } |
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