From 63e03c0b5bb737da1fe44502cf8ad92ee28dc773 Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Thu, 8 Jun 2023 09:57:54 +0100 Subject: [PATCH 1/3] Add singularity.registry = 'quay.io' for tests --- modules/nf-core/fastqc/main.nf | 6 +++++- modules/nf-core/gatk4/applybqsrspark/main.nf | 4 +++- tests/config/nextflow.config | 1 + tests/config/nf-test.config | 1 + 4 files changed, 10 insertions(+), 2 deletions(-) diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf index 07d5e433128..249f90644d2 100644 --- a/modules/nf-core/fastqc/main.nf +++ b/modules/nf-core/fastqc/main.nf @@ -29,7 +29,11 @@ process FASTQC { printf "%s %s\\n" $rename_to | while read old_name new_name; do [ -f "\${new_name}" ] || ln -s \$old_name \$new_name done - fastqc $args --threads $task.cpus $renamed_files + + fastqc \\ + $args \\ + --threads $task.cpus \\ + $renamed_files cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/gatk4/applybqsrspark/main.nf b/modules/nf-core/gatk4/applybqsrspark/main.nf index 88ead471c8c..6451b1bad4d 100644 --- a/modules/nf-core/gatk4/applybqsrspark/main.nf +++ b/modules/nf-core/gatk4/applybqsrspark/main.nf @@ -31,7 +31,9 @@ process GATK4_APPLYBQSR_SPARK { avail_mem = (task.memory.mega*0.8).intValue() } """ - gatk --java-options "-Xmx${avail_mem}M" ApplyBQSRSpark \\ + gatk \\ + --java-options "-Xmx${avail_mem}M" \\ + ApplyBQSRSpark \\ --input $input \\ --output ${prefix}.${input.getExtension()} \\ --reference $fasta \\ diff --git a/tests/config/nextflow.config b/tests/config/nextflow.config index b6db38865d9..06216f192eb 100644 --- a/tests/config/nextflow.config +++ b/tests/config/nextflow.config @@ -13,6 +13,7 @@ process { if ("$PROFILE" == "singularity") { singularity.enabled = true + singularity.registry = 'quay.io' singularity.autoMounts = true } else if ("$PROFILE" == "conda") { conda.enabled = true diff --git a/tests/config/nf-test.config b/tests/config/nf-test.config index a460022ee50..cde74eedd3a 100644 --- a/tests/config/nf-test.config +++ b/tests/config/nf-test.config @@ -14,6 +14,7 @@ process { profiles { singularity { singularity.enabled = true + singularity.registry = 'quay.io' singularity.autoMounts = true } conda { From b718fa9b53ab161ab6ac2314cd43a839d55ca62f Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Thu, 8 Jun 2023 10:01:17 +0100 Subject: [PATCH 2/3] Bump min NF version to 23.04.0 --- tests/config/nextflow.config | 2 +- tests/config/nf-test.config | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/tests/config/nextflow.config b/tests/config/nextflow.config index 06216f192eb..ba10dfe5e4d 100644 --- a/tests/config/nextflow.config +++ b/tests/config/nextflow.config @@ -39,5 +39,5 @@ conda { createTimeout = "120 min" } includeConfig 'test_data.config' manifest { - nextflowVersion = '!>=22.10.1' + nextflowVersion = '!>=23.04.0' } diff --git a/tests/config/nf-test.config b/tests/config/nf-test.config index cde74eedd3a..83000e5bf66 100644 --- a/tests/config/nf-test.config +++ b/tests/config/nf-test.config @@ -45,5 +45,5 @@ conda { createTimeout = "120 min" } includeConfig 'test_data.config' manifest { - nextflowVersion = '!>=22.10.1' + nextflowVersion = '!>=23.04.0' } From ea8564e9618b7c725bd3942efe84dda0e29854d3 Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Thu, 8 Jun 2023 16:52:14 +0100 Subject: [PATCH 3/3] Move registry definitions to top-level config scope --- tests/config/nextflow.config | 7 ++++--- tests/config/nf-test.config | 7 ++++--- 2 files changed, 8 insertions(+), 6 deletions(-) diff --git a/tests/config/nextflow.config b/tests/config/nextflow.config index ba10dfe5e4d..104f1d9e57a 100644 --- a/tests/config/nextflow.config +++ b/tests/config/nextflow.config @@ -13,7 +13,6 @@ process { if ("$PROFILE" == "singularity") { singularity.enabled = true - singularity.registry = 'quay.io' singularity.autoMounts = true } else if ("$PROFILE" == "conda") { conda.enabled = true @@ -22,16 +21,18 @@ if ("$PROFILE" == "singularity") { conda.useMamba = true } else if ("$PROFILE" == "podman") { podman.enabled = true - podman.registry = 'quay.io' podman.userEmulation = true podman.runOptions = "--runtime crun --platform linux/x86_64 --systemd=always" } else { docker.enabled = true - docker.registry = 'quay.io' docker.userEmulation = true docker.runOptions = "--platform linux/x86_64" } +docker.registry = 'quay.io' +podman.registry = 'quay.io' +singularity.registry = 'quay.io' + // Increase time available to build Conda environment conda { createTimeout = "120 min" } diff --git a/tests/config/nf-test.config b/tests/config/nf-test.config index 83000e5bf66..a3765047417 100644 --- a/tests/config/nf-test.config +++ b/tests/config/nf-test.config @@ -14,7 +14,6 @@ process { profiles { singularity { singularity.enabled = true - singularity.registry = 'quay.io' singularity.autoMounts = true } conda { @@ -26,18 +25,20 @@ profiles { } podman { podman.enabled = true - podman.registry = 'quay.io' podman.userEmulation = true podman.runOptions = "--runtime crun --platform linux/x86_64 --systemd=always" } docker { docker.enabled = true - docker.registry = 'quay.io' docker.userEmulation = true docker.runOptions = "--platform linux/x86_64" } } +docker.registry = 'quay.io' +podman.registry = 'quay.io' +singularity.registry = 'quay.io' + // Increase time available to build Conda environment conda { createTimeout = "120 min" }