diff --git a/modules.json b/modules.json index 94ded5a..d77d640 100644 --- a/modules.json +++ b/modules.json @@ -7,12 +7,12 @@ "gallvp": { "agat/spaddintrons": { "branch": "main", - "git_sha": "7bf6fbca23edc94490ffa6709f52b2f71c6fb130", + "git_sha": "004aba06875a2fee13207e2ffaa04deb2190a35d", "installed_by": ["gxf_fasta_agat_spaddintrons_spextractsequences"] }, "agat/spextractsequences": { "branch": "main", - "git_sha": "7bf6fbca23edc94490ffa6709f52b2f71c6fb130", + "git_sha": "004aba06875a2fee13207e2ffaa04deb2190a35d", "installed_by": ["gxf_fasta_agat_spaddintrons_spextractsequences"] }, "braker3": { @@ -22,22 +22,22 @@ }, "busco/busco": { "branch": "main", - "git_sha": "ab92c438688c1f4a3753b65914bfd2e6319cebb2", + "git_sha": "0fcdaa66410acee08d31884cdc3e8e4b1b79e66a", "installed_by": ["fasta_gxf_busco_plot"] }, "busco/generateplot": { "branch": "main", - "git_sha": "ab92c438688c1f4a3753b65914bfd2e6319cebb2", + "git_sha": "004aba06875a2fee13207e2ffaa04deb2190a35d", "installed_by": ["fasta_gxf_busco_plot"] }, "custom/restoregffids": { "branch": "main", - "git_sha": "490f8ab54c632d84f99edd6f208305ac5e283ab3", + "git_sha": "004aba06875a2fee13207e2ffaa04deb2190a35d", "installed_by": ["fasta_edta_lai"] }, "custom/shortenfastaids": { "branch": "main", - "git_sha": "490f8ab54c632d84f99edd6f208305ac5e283ab3", + "git_sha": "004aba06875a2fee13207e2ffaa04deb2190a35d", "installed_by": ["fasta_edta_lai"] }, "edta/edta": { @@ -47,17 +47,17 @@ }, "gffread": { "branch": "main", - "git_sha": "c04bf39d67027e044a6eaed0b7b0439fd8866fc7", + "git_sha": "004aba06875a2fee13207e2ffaa04deb2190a35d", "installed_by": ["fasta_gxf_busco_plot"] }, "ltrretriever/lai": { "branch": "main", - "git_sha": "490f8ab54c632d84f99edd6f208305ac5e283ab3", + "git_sha": "004aba06875a2fee13207e2ffaa04deb2190a35d", "installed_by": ["fasta_edta_lai"] }, "repeatmasker/repeatmasker": { "branch": "main", - "git_sha": "07c6fda11aff03d2d7fc68224e7fd96866fc6a8f", + "git_sha": "004aba06875a2fee13207e2ffaa04deb2190a35d", "installed_by": ["modules"] } } @@ -132,7 +132,7 @@ }, "fastqc": { "branch": "master", - "git_sha": "46eca555142d6e597729fcb682adcc791796f514", + "git_sha": "b49b8992e5271ce427f3a7cdb29628fc58400eb5", "installed_by": ["fastq_fastqc_umitools_fastp", "modules"] }, "gffcompare": { @@ -168,12 +168,12 @@ }, "repeatmodeler/builddatabase": { "branch": "master", - "git_sha": "1cbb5551b917aa423e414dcd69898d01520a309d", + "git_sha": "52507581f62929f98dd6e6c5c5824583fa6ef94d", "installed_by": ["modules"] }, "repeatmodeler/repeatmodeler": { "branch": "master", - "git_sha": "84efd2f87d07deb22ee9378f065a9aa5f1434161", + "git_sha": "52507581f62929f98dd6e6c5c5824583fa6ef94d", "installed_by": ["modules"] }, "samtools/cat": { diff --git a/modules/gallvp/agat/spaddintrons/environment.yml b/modules/gallvp/agat/spaddintrons/environment.yml index 854ee35..f108584 100644 --- a/modules/gallvp/agat/spaddintrons/environment.yml +++ b/modules/gallvp/agat/spaddintrons/environment.yml @@ -4,6 +4,6 @@ name: "agat_spaddintrons" channels: - conda-forge - bioconda - - defaults + dependencies: - "bioconda::agat=1.4.0" diff --git a/modules/gallvp/agat/spextractsequences/environment.yml b/modules/gallvp/agat/spextractsequences/environment.yml index be40401..c164fc0 100644 --- a/modules/gallvp/agat/spextractsequences/environment.yml +++ b/modules/gallvp/agat/spextractsequences/environment.yml @@ -4,6 +4,6 @@ name: "agat_spextractsequences" channels: - conda-forge - bioconda - - defaults + dependencies: - bioconda::agat=1.4.0 diff --git a/modules/gallvp/busco/busco/environment.yml b/modules/gallvp/busco/busco/environment.yml index 06a5d93..7df4e9a 100644 --- a/modules/gallvp/busco/busco/environment.yml +++ b/modules/gallvp/busco/busco/environment.yml @@ -2,6 +2,6 @@ name: busco_busco channels: - conda-forge - bioconda - - defaults + dependencies: - bioconda::busco=5.7.1 diff --git a/modules/gallvp/busco/busco/tests/main.nf.test b/modules/gallvp/busco/busco/tests/main.nf.test index 829bd28..e0eb735 100644 --- a/modules/gallvp/busco/busco/tests/main.nf.test +++ b/modules/gallvp/busco/busco/tests/main.nf.test @@ -126,7 +126,7 @@ nextflow_process { } assert snapshot( - process.out.batch_summary[0][1], + file(process.out.batch_summary[0][1]).name, process.out.full_table[0][1], process.out.missing_busco_list[0][1], process.out.versions[0] diff --git a/modules/gallvp/busco/busco/tests/main.nf.test.snap b/modules/gallvp/busco/busco/tests/main.nf.test.snap index 1b6411b..1140d5d 100644 --- a/modules/gallvp/busco/busco/tests/main.nf.test.snap +++ b/modules/gallvp/busco/busco/tests/main.nf.test.snap @@ -146,7 +146,7 @@ }, "test_busco_genome_multi_fasta": { "content": [ - "test-bacteria_odb10-busco.batch_summary.txt:md5,fcd3c208913e8abda3d6742c43fec5fa", + "test-bacteria_odb10-busco.batch_summary.txt", [ "full_table.tsv:md5,c657edcc7d0de0175869717551df6e83", "full_table.tsv:md5,638fe7590f442c57361554dae330eca1" @@ -159,9 +159,9 @@ ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "24.04.4" }, - "timestamp": "2024-05-03T13:23:50.255602" + "timestamp": "2024-08-22T11:24:24.828742" }, "test_busco_eukaryote_metaeuk": { "content": [ diff --git a/modules/gallvp/busco/generateplot/environment.yml b/modules/gallvp/busco/generateplot/environment.yml index 1ca5bab..eb97426 100644 --- a/modules/gallvp/busco/generateplot/environment.yml +++ b/modules/gallvp/busco/generateplot/environment.yml @@ -4,6 +4,6 @@ name: "busco_generateplot" channels: - conda-forge - bioconda - - defaults + dependencies: - bioconda::busco=5.7.1 diff --git a/modules/gallvp/custom/restoregffids/environment.yml b/modules/gallvp/custom/restoregffids/environment.yml index 2450c45..a13fdbb 100644 --- a/modules/gallvp/custom/restoregffids/environment.yml +++ b/modules/gallvp/custom/restoregffids/environment.yml @@ -4,6 +4,6 @@ name: "custom_restoregffids" channels: - conda-forge - bioconda - - defaults + dependencies: - "python=3.10.2" diff --git a/modules/gallvp/custom/shortenfastaids/environment.yml b/modules/gallvp/custom/shortenfastaids/environment.yml index a64758c..2d7b9f7 100644 --- a/modules/gallvp/custom/shortenfastaids/environment.yml +++ b/modules/gallvp/custom/shortenfastaids/environment.yml @@ -4,7 +4,6 @@ name: "custom_shortenfastaids" channels: - conda-forge - bioconda - - defaults dependencies: - biopython==1.75 diff --git a/modules/gallvp/gffread/environment.yml b/modules/gallvp/gffread/environment.yml index c6df58a..5575384 100644 --- a/modules/gallvp/gffread/environment.yml +++ b/modules/gallvp/gffread/environment.yml @@ -2,6 +2,6 @@ name: gffread channels: - conda-forge - bioconda - - defaults + dependencies: - bioconda::gffread=0.12.7 diff --git a/modules/gallvp/ltrretriever/lai/environment.yml b/modules/gallvp/ltrretriever/lai/environment.yml index e0e4968..b55c28a 100644 --- a/modules/gallvp/ltrretriever/lai/environment.yml +++ b/modules/gallvp/ltrretriever/lai/environment.yml @@ -4,6 +4,6 @@ name: "ltrretriever_lai" channels: - conda-forge - bioconda - - defaults + dependencies: - "bioconda::LTR_retriever=2.9.9" diff --git a/modules/gallvp/repeatmasker/repeatmasker/environment.yml b/modules/gallvp/repeatmasker/repeatmasker/environment.yml index efc290a..d701a5c 100644 --- a/modules/gallvp/repeatmasker/repeatmasker/environment.yml +++ b/modules/gallvp/repeatmasker/repeatmasker/environment.yml @@ -4,6 +4,6 @@ name: "repeatmasker_repeatmasker" channels: - conda-forge - bioconda - - defaults + dependencies: - "bioconda::repeatmasker=4.1.5" diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf index d79f1c8..d8989f4 100644 --- a/modules/nf-core/fastqc/main.nf +++ b/modules/nf-core/fastqc/main.nf @@ -26,7 +26,10 @@ process FASTQC { def rename_to = old_new_pairs*.join(' ').join(' ') def renamed_files = old_new_pairs.collect{ old_name, new_name -> new_name }.join(' ') - def memory_in_mb = MemoryUnit.of("${task.memory}").toUnit('MB') + // The total amount of allocated RAM by FastQC is equal to the number of threads defined (--threads) time the amount of RAM defined (--memory) + // https://github.com/s-andrews/FastQC/blob/1faeea0412093224d7f6a07f777fad60a5650795/fastqc#L211-L222 + // Dividing the task.memory by task.cpu allows to stick to requested amount of RAM in the label + def memory_in_mb = MemoryUnit.of("${task.memory}").toUnit('MB') / task.cpus // FastQC memory value allowed range (100 - 10000) def fastqc_memory = memory_in_mb > 10000 ? 10000 : (memory_in_mb < 100 ? 100 : memory_in_mb) diff --git a/modules/nf-core/repeatmodeler/builddatabase/tests/main.nf.test b/modules/nf-core/repeatmodeler/builddatabase/tests/main.nf.test index bfe5d78..78b78a6 100644 --- a/modules/nf-core/repeatmodeler/builddatabase/tests/main.nf.test +++ b/modules/nf-core/repeatmodeler/builddatabase/tests/main.nf.test @@ -16,7 +16,7 @@ nextflow_process { """ input[0] = [ [ id:'test' ], // meta map - file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] """ } @@ -42,7 +42,7 @@ nextflow_process { """ input[0] = [ [ id:'test' ], // meta map - file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] """ } diff --git a/modules/nf-core/repeatmodeler/repeatmodeler/tests/main.nf.test b/modules/nf-core/repeatmodeler/repeatmodeler/tests/main.nf.test index 65edd7e..829e222 100644 --- a/modules/nf-core/repeatmodeler/repeatmodeler/tests/main.nf.test +++ b/modules/nf-core/repeatmodeler/repeatmodeler/tests/main.nf.test @@ -20,7 +20,7 @@ nextflow_process { """ input[0] = [ [ id:'test' ], // meta map - file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ] """ } @@ -56,7 +56,7 @@ nextflow_process { """ input[0] = [ [ id:'test' ], // meta map - file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ] """ }