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Refactor all configs. Use singularity for UPPMAX.
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| Original file line number | Diff line number | Diff line change |
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| @@ -1,4 +1,5 @@ | ||
| FROM openjdk:8 | ||
| # openjdk:8 moved from debian jessie to stretch after u131, which breaks everything (bowtie) | ||
| FROM openjdk:8u121 | ||
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| LABEL authors="[email protected],[email protected]" \ | ||
| description="Docker image containing all requirements for NGI-MethylSeq pipeline" | ||
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@@ -89,3 +90,6 @@ RUN mkdir /opt/MethylDackel && \ | |
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| # Install MultiQC | ||
| RUN pip install multiqc | ||
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| # Create UPPMAX directories for Singularity | ||
| RUN mkdir /pica /proj /sw | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,92 @@ | ||
| /* | ||
| vim: syntax=groovy | ||
| -*- mode: groovy;-*- | ||
| * ------------------------------------------------- | ||
| * Base Nextflow config file | ||
| * ------------------------------------------------- | ||
| * This file contains basic process requirement setup | ||
| * It DOES NOT contain any config for cluster, so will run | ||
| * in default mode by itself. It should be used with | ||
| * the max_memory, max_cpus and max_time params for | ||
| * customising hardware limits | ||
| */ | ||
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| process { | ||
| cpus = { check_max(1 * task.attempt, 'cpus') } | ||
| memory = { check_max( 8.GB * task.attempt, 'memory') } | ||
| time = { check_max(2.h * task.attempt, 'time') } | ||
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| errorStrategy = { ( task.exitStatus == 143 || task.exitStatus == 137 ) ? 'retry' : 'finish' } | ||
| maxRetries = 3 | ||
| maxErrors = '-1' | ||
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| // Resource requirements | ||
| $makeBismarkIndex { | ||
| cpus = { check_max(8 * task.attempt, 'cpus') } | ||
| memory = { check_max( 64.GB * task.attempt, 'memory') } | ||
| time = { check_max(36.h * task.attempt, 'time') } | ||
| } | ||
| $fastqc { | ||
| errorStrategy = { ( task.exitStatus == 143 || task.exitStatus == 137 ) ? 'retry' : 'ignore' } | ||
| } | ||
| $trim_galore { | ||
| cpus = { check_max(2 * task.attempt, 'cpus') } | ||
| memory = { check_max( 16.GB * task.attempt, 'memory') } | ||
| time = { check_max(12.h * task.attempt, 'time') } | ||
| } | ||
| $bismark_align { | ||
| cpus = { check_max(8 * task.attempt, 'cpus') } | ||
| memory = { check_max( 64.GB * task.attempt, 'memory') } | ||
| time = { check_max(36.h * task.attempt, 'time') } | ||
| } | ||
| $bismark_deduplicate { | ||
| cpus = { check_max(8 * task.attempt, 'cpus') } | ||
| memory = { check_max( 64.GB * task.attempt, 'memory') } | ||
| time = { check_max(12.h * task.attempt, 'time') } | ||
| } | ||
| $bismark_methXtract { | ||
| cpus = { check_max(4 * task.attempt, 'cpus') } | ||
| memory = { check_max( 32.GB * task.attempt, 'memory') } | ||
| time = { check_max(8.h * task.attempt, 'time') } | ||
| } | ||
| $bismark_report { | ||
| errorStrategy = { ( task.exitStatus == 143 || task.exitStatus == 137 ) ? 'retry' : 'ignore' } | ||
| } | ||
| $bismark_summary { | ||
| errorStrategy = { ( task.exitStatus == 143 || task.exitStatus == 137 ) ? 'retry' : 'ignore' } | ||
| } | ||
| $qualimap { | ||
| cpus = { check_max(4 * task.attempt, 'cpus') } | ||
| memory = { check_max( 32.GB * task.attempt, 'memory') } | ||
| time = { check_max(6.h * task.attempt, 'time') } | ||
| errorStrategy = { ( task.exitStatus == 143 || task.exitStatus == 137 ) ? 'retry' : 'ignore' } | ||
| } | ||
| $get_software_versions { | ||
| executor = 'local' | ||
| errorStrategy = 'ignore' | ||
| } | ||
| $multiqc { | ||
| executor = 'local' | ||
| errorStrategy = { ( task.exitStatus == 143 || task.exitStatus == 137 ) ? 'retry' : 'ignore' } | ||
| } | ||
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| $bwamem_align { | ||
| cpus = { check_max(8 * task.attempt, 'cpus') } | ||
| memory = { check_max( 64.GB * task.attempt, 'memory') } | ||
| time = { check_max(24.h * task.attempt, 'time') } | ||
| } | ||
| $samtools_sort { | ||
| cpus = { check_max(4 * task.attempt, 'cpus') } | ||
| memory = { check_max( 32.GB * task.attempt, 'memory') } | ||
| time = { check_max(8.h * task.attempt, 'time') } | ||
| } | ||
| $markDuplicates { | ||
| cpus = { check_max(4 * task.attempt, 'cpus') } | ||
| memory = { check_max( 32.GB * task.attempt, 'memory') } | ||
| } | ||
| $methyldackel { | ||
| cpus = { check_max(6 * task.attempt, 'cpus') } | ||
| memory = { check_max( 48.GB * task.attempt, 'memory') } | ||
| } | ||
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| } |
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