diff --git a/modules/custom/dumpsoftwareversions/main.nf b/modules/custom/dumpsoftwareversions/main.nf index 34b50b9f..cebb6e05 100644 --- a/modules/custom/dumpsoftwareversions/main.nf +++ b/modules/custom/dumpsoftwareversions/main.nf @@ -2,10 +2,10 @@ process CUSTOM_DUMPSOFTWAREVERSIONS { label 'process_single' // Requires `pyyaml` which does not have a dedicated container but is in the MultiQC container - conda (params.enable_conda ? 'bioconda::multiqc=1.13a' : null) + conda (params.enable_conda ? 'bioconda::multiqc=1.13' : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.13a--pyhdfd78af_1' : - 'quay.io/biocontainers/multiqc:1.13a--pyhdfd78af_1' }" + 'https://depot.galaxyproject.org/singularity/multiqc:1.13--pyhdfd78af_0' : + 'quay.io/biocontainers/multiqc:1.13--pyhdfd78af_0' }" input: path versions diff --git a/modules/qualimap/rnaseq/main.nf b/modules/qualimap/rnaseq/main.nf index bd4503b2..38293d27 100644 --- a/modules/qualimap/rnaseq/main.nf +++ b/modules/qualimap/rnaseq/main.nf @@ -20,7 +20,7 @@ process QUALIMAP_RNASEQ { script: def args = task.ext.args ?: '' - def prefix = task.ext.prefix ?: "${meta.id}" + prefix = task.ext.prefix ?: "${meta.id}" def paired_end = meta.single_end ? '' : '-pe' def memory = task.memory.toGiga() + "G" @@ -51,7 +51,7 @@ process QUALIMAP_RNASEQ { """ stub: - def prefix = task.ext.prefix ?: "${meta.id}" + prefix = task.ext.prefix ?: "${meta.id}" """ mkdir ${prefix} diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml index 51bd3ed2..9e66b1d7 100644 --- a/tests/config/pytest_modules.yml +++ b/tests/config/pytest_modules.yml @@ -2363,10 +2363,6 @@ tbprofiler/profile: - modules/tbprofiler/profile/** - tests/modules/tbprofiler/profile/** -test/template: - - modules/test/template/** - - tests/modules/test/template/** - tiddit/cov: - modules/tiddit/cov/** - tests/modules/tiddit/cov/** diff --git a/tests/config/pytest_modules_test.yml b/tests/config/pytest_modules_test.yml deleted file mode 100644 index eba3c1cc..00000000 --- a/tests/config/pytest_modules_test.yml +++ /dev/null @@ -1,23 +0,0 @@ -abacas: - - modules/abacas/** - - tests/modules/abacas/** - -kallisto/index: - - modules/kallisto/index/** - - tests/modules/kallisto/index/** - -kallistobustools/count: - - modules/kallistobustools/count/** - - tests/modules/kallistobustools/count/** - -kallistobustools/ref: - - modules/kallistobustools/ref/** - - tests/modules/kallistobustools/ref/** - -kat/hist: - - modules/kat/hist/** - - tests/modules/kat/hist/** - -spades: - - modules/spades/** - - tests/modules/spades/**