diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml index ef39ca436861..ab1fd88d1fb4 100644 --- a/.github/workflows/nf-test.yml +++ b/.github/workflows/nf-test.yml @@ -77,7 +77,7 @@ jobs: env: NFT_VER: ${{ env.NFT_VER }} with: - max_shards: 16 + max_shards: 60 paths: "${{ join(fromJson(steps.list.outputs.components ), ' ') }}" - name: debug diff --git a/modules/nf-core/cellrangerarc/mkfastq/main.nf b/modules/nf-core/cellrangerarc/mkfastq/main.nf index d01124bf1bd7..a29040cc0cd7 100644 --- a/modules/nf-core/cellrangerarc/mkfastq/main.nf +++ b/modules/nf-core/cellrangerarc/mkfastq/main.nf @@ -28,7 +28,7 @@ process CELLRANGERARC_MKFASTQ { """ cellranger-arc mkfastq --id=${prefix} \\ --localmem=${task.memory.toGiga()} \\ - --localcores=${task.cpus} \\ + --localcores=1 \\ --run=${bcl} \\ --csv=${csv} \\ ${args} diff --git a/modules/nf-core/foldmason/msa2lddtreport/tests/main.nf.test b/modules/nf-core/foldmason/msa2lddtreport/tests/main.nf.test index b92c05d0704c..1cdd45ee8c89 100644 --- a/modules/nf-core/foldmason/msa2lddtreport/tests/main.nf.test +++ b/modules/nf-core/foldmason/msa2lddtreport/tests/main.nf.test @@ -39,7 +39,7 @@ nextflow_process { script "../../../../../modules/nf-core/foldmason/createdb/main.nf" process { """ - input[0] = UNTAR.out.untar.map { meta,dir -> [meta, file(dir).listFiles().collect()]} + input[0] = UNTAR.out.untar.map { meta,dir -> [meta, file(dir).listFiles().sort().collect()]} """ } } @@ -57,7 +57,7 @@ nextflow_process { file(params.modules_testdata_base_path + "../../multiplesequencealign/testdata/setoxin.ref", checkIfExists: true) ] input[1] = FOLDMASON_CREATEDB.out.db.collect{ meta, db -> db }.map{ db -> [[ id: 'test'], db]} - input[2] = UNTAR.out.untar.map { meta,dir -> [meta, file(dir).listFiles().collect()]} + input[2] = UNTAR.out.untar.map { meta,dir -> [meta, file(dir).listFiles().sort().collect()]} input[3] = FAMSA_GUIDETREE.out.tree.collect{ meta, tree -> tree }.map{ tree -> [[ id: 'test_tree'], tree]} """ } @@ -83,7 +83,7 @@ nextflow_process { file(params.modules_testdata_base_path + "../../multiplesequencealign/testdata/setoxin.ref", checkIfExists: true) ] input[1] = FOLDMASON_CREATEDB.out.db.collect{ meta, db -> db }.map{ db -> [[ id: 'test'], db]} - input[2] = UNTAR.out.untar.map { meta,dir -> [meta, file(dir).listFiles().collect()]} + input[2] = UNTAR.out.untar.map { meta,dir -> [meta, file(dir).listFiles().sort().collect()]} input[3] = FAMSA_GUIDETREE.out.tree.collect{ meta, tree -> tree }.map{ tree -> [[ id: 'test_tree'], tree]} """ } diff --git a/modules/nf-core/orthofinder/environment.yml b/modules/nf-core/orthofinder/environment.yml index 7696be75a0c5..a1d3c2dde731 100644 --- a/modules/nf-core/orthofinder/environment.yml +++ b/modules/nf-core/orthofinder/environment.yml @@ -6,3 +6,4 @@ channels: dependencies: - bioconda::diamond=2.1.9 - bioconda::orthofinder=2.5.5 + - conda-forge::python=3.10.* # orthofinder 2.5.5 supported only up to python 3.10 diff --git a/modules/nf-core/untar/main.nf b/modules/nf-core/untar/main.nf index e712ebe63ab5..a09bb007063a 100644 --- a/modules/nf-core/untar/main.nf +++ b/modules/nf-core/untar/main.nf @@ -30,6 +30,7 @@ process UNTAR { if [[ \$(tar -taf ${archive} | grep -o -P "^.*?\\/" | uniq | wc -l) -eq 1 ]]; then tar \\ -C ${prefix} --strip-components 1 \\ + --no-same-owner \\ -xavf \\ ${args} \\ ${archive} \\ @@ -37,6 +38,7 @@ process UNTAR { else tar \\ -C ${prefix} \\ + --no-same-owner \\ -xavf \\ ${args} \\ ${archive} \\