From fb30e09a9353c924308154662c1185d6125f5807 Mon Sep 17 00:00:00 2001 From: Nate Coraor Date: Mon, 4 Nov 2024 18:00:19 -0500 Subject: [PATCH] Replace noqas with FIXMEs --- tools.yml | 57 +++++++++++++++++++++++++++++-------------------------- 1 file changed, 30 insertions(+), 27 deletions(-) diff --git a/tools.yml b/tools.yml index 38d360c..05134f2 100644 --- a/tools.yml +++ b/tools.yml @@ -31,10 +31,10 @@ tools: cores: 1 mem: 20 toolshed.g2.bx.psu.edu/repos/artbio/repenrich/repenrich/.*: - # noqa: T102 + # FIXME: needs mem cores: 8 toolshed.g2.bx.psu.edu/repos/bebatut/cdhit/cd_hit_est/.*: - # noqa: T102 + # FIXME: needs mem cores: 4 toolshed.g2.bx.psu.edu/repos/bgruening/alevin/alevin/.*: cores: 8 @@ -261,7 +261,7 @@ tools: cores: 5 mem: 12 toolshed.g2.bx.psu.edu/repos/bgruening/nanopolish_polya/nanopolish_polya/.*: - # noqa: T102 + # FIXME: needs mem cores: 3 toolshed.g2.bx.psu.edu/repos/bgruening/nanopolish_variants/nanopolish_variants/.*: cores: 5 @@ -586,12 +586,12 @@ tools: cores: 24 mem: 200 toolshed.g2.bx.psu.edu/repos/galaxy-australia/dorado_pod5_convert/dorado_pod5_convert/.*: - # noqa: T102 + # FIXME: needs mem cores: 8 toolshed.g2.bx.psu.edu/repos/galaxy-australia/hapcut2/hapcut2/.*: mem: 8 toolshed.g2.bx.psu.edu/repos/galaxy-australia/hifiadapterfilt/hifiadapterfilt/.*: - # noqa: T102 + # FIXME: needs mem cores: 12 toolshed.g2.bx.psu.edu/repos/galaxy-australia/hifiasm_meta/hifiasm_meta/.*: cores: 16 @@ -1059,16 +1059,16 @@ tools: toolshed.g2.bx.psu.edu/repos/galaxyp/uniprotxml_downloader/uniprotxml_downloader/.*: mem: 8 toolshed.g2.bx.psu.edu/repos/gbcs-embl-heidelberg/je_clip/je_clip/.*: - # noqa: T102 + # FIXME: needs mem cores: 8 toolshed.g2.bx.psu.edu/repos/gbcs-embl-heidelberg/je_demultiplex/je_demultiplex/.*: cores: 8 mem: 20 toolshed.g2.bx.psu.edu/repos/gbcs-embl-heidelberg/je_demultiplex_illu/je_demultiplex_illu/.*: - # noqa: T102 + # FIXME: needs mem cores: 8 toolshed.g2.bx.psu.edu/repos/gbcs-embl-heidelberg/je_markdupes/je_markdupes/.*: - # noqa: T102 + # FIXME: needs mem cores: 8 toolshed.g2.bx.psu.edu/repos/genouest/braker3/braker3/.*: cores: 16 @@ -1088,6 +1088,9 @@ tools: mem: 12 env: _JAVA_OPTIONS: -Xmx{int(mem)}G -Xms1G + toolshed.g2.bx.psu.edu/repos/iuc/extract_genomic_dna/Extract genomic DNA 1: + cores: 3 + mem: 3.7 toolshed.g2.bx.psu.edu/repos/iuc/abricate/abricate/.*: mem: 30.4 toolshed.g2.bx.psu.edu/repos/iuc/abyss/abyss-pe/.*: @@ -1116,7 +1119,7 @@ tools: toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_info/.*: mem: 16 toolshed.g2.bx.psu.edu/repos/iuc/barrnap/barrnap/.*: - # noqa: T102 + # FIXME: needs mem cores: 3 toolshed.g2.bx.psu.edu/repos/iuc/bbtools_callvariants/bbtools_callvariants/.*: mem: 15 @@ -1235,6 +1238,7 @@ tools: mem: 11.4 toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/.*: cores: 4 + mem: toolshed.g2.bx.psu.edu/repos/iuc/fasttree/fasttree/.*: mem: 30 rules: @@ -2176,7 +2180,7 @@ tools: if: input_size < 0.2 mem: 8 toolshed.g2.bx.psu.edu/repos/iuc/ont_fast5_api_compress_fast5/ont_fast5_api_compress_fast5/.*: - # noqa: T102 + # FIXME: needs mem cores: 8 toolshed.g2.bx.psu.edu/repos/iuc/orfipy/orfipy/.*: cores: 8 @@ -2252,7 +2256,7 @@ tools: cores: 10 mem: 12 toolshed.g2.bx.psu.edu/repos/iuc/raven/raven/.*: - # noqa: T102 + # FIXME: needs mem cores: 16 toolshed.g2.bx.psu.edu/repos/iuc/raxml/raxml/.*: cores: 16 @@ -2411,32 +2415,32 @@ tools: toolshed.g2.bx.psu.edu/repos/iuc/stacks2_clonefilter/stacks2_clonefilter/.*: mem: 8 toolshed.g2.bx.psu.edu/repos/iuc/stacks2_cstacks/stacks2_cstacks/.*: - # noqa: T102 + # FIXME: needs mem cores: 16 toolshed.g2.bx.psu.edu/repos/iuc/stacks2_denovomap/stacks2_denovomap/.*: cores: 4 mem: 16 toolshed.g2.bx.psu.edu/repos/iuc/stacks2_gstacks/stacks2_gstacks/.*: - # noqa: T102 + # FIXME: needs mem cores: 16 toolshed.g2.bx.psu.edu/repos/iuc/stacks2_kmerfilter/stacks2_kmerfilter/.*: mem: 7.6 toolshed.g2.bx.psu.edu/repos/iuc/stacks2_populations/stacks2_populations/.*: - # noqa: T102 + # FIXME: needs mem cores: 8 toolshed.g2.bx.psu.edu/repos/iuc/stacks2_refmap/stacks2_refmap/.*: - # noqa: T102 + # FIXME: needs mem cores: 8 toolshed.g2.bx.psu.edu/repos/iuc/stacks2_shortreads/stacks2_shortreads/.*: mem: 7.6 toolshed.g2.bx.psu.edu/repos/iuc/stacks2_sstacks/stacks2_sstacks/.*: - # noqa: T102 + # FIXME: needs mem cores: 16 toolshed.g2.bx.psu.edu/repos/iuc/stacks2_tsv2bam/stacks2_tsv2bam/.*: cores: 8 mem: 42 toolshed.g2.bx.psu.edu/repos/iuc/stacks2_ustacks/stacks2_ustacks/.*: - # noqa: T102 + # FIXME: needs mem cores: 16 toolshed.g2.bx.psu.edu/repos/iuc/stacks_clonefilter/stacks_clonefilter/.*: mem: 8 @@ -2471,19 +2475,19 @@ tools: toolshed.g2.bx.psu.edu/repos/iuc/trinity_run_de_analysis/trinity_run_de_analysis/.*: mem: 15 toolshed.g2.bx.psu.edu/repos/iuc/trycycler_cluster/trycycler_cluster/.*: - # noqa: T102 + # FIXME: needs mem cores: 9 toolshed.g2.bx.psu.edu/repos/iuc/trycycler_consensus/trycycler_consensus/.*: - # noqa: T102 + # FIXME: needs mem cores: 16 toolshed.g2.bx.psu.edu/repos/iuc/trycycler_partition/trycycler_partition/.*: - # noqa: T102 + # FIXME: needs mem cores: 9 toolshed.g2.bx.psu.edu/repos/iuc/trycycler_reconcile_msa/trycycler_reconcile_msa/.*: - # noqa: T102 + # FIXME: needs mem cores: 9 toolshed.g2.bx.psu.edu/repos/iuc/trycycler_subsample/trycycler_subsample/.*: - # noqa: T102 + # FIXME: needs mem cores: 9 toolshed.g2.bx.psu.edu/repos/iuc/ucsc_wigtobigwig/ucsc_wigtobigwig/.*: mem: 20 @@ -2542,7 +2546,8 @@ tools: toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_retcor/abims_xcms_retcor/.*: mem: 32 toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/.*: - cores: 5 + cores: 8 + mem: 28 toolshed.g2.bx.psu.edu/repos/lparsons/htseq_count/htseq_count/.*: mem: 32 toolshed.g2.bx.psu.edu/repos/mbernt/maxbin2/maxbin2/.*: @@ -2608,7 +2613,7 @@ tools: cores: 4 mem: 32 toolshed.g2.bx.psu.edu/repos/recetox/recetox_aplcms_align_features/recetox_aplcms_align_features/.*: - # noqa: T102 + # FIXME: needs mem cores: 4 toolshed.g2.bx.psu.edu/repos/recetox/recetox_aplcms_generate_feature_table/recetox_aplcms_generate_feature_table/.*: mem: 16 @@ -2660,7 +2665,7 @@ tools: cores: 12 mem: 16 toolshed.g2.bx.psu.edu/repos/rnateam/rnalien/RNAlien/.*: - # noqa: T102 + # FIXME: needs mem cores: 10 toolshed.g2.bx.psu.edu/repos/rnateam/segemehl/segemehl/.*: mem: 80 @@ -2756,8 +2761,6 @@ tools: mem: 36 CONVERTER_bedgraph_to_bigwig: mem: 8 - Extract genomic DNA 1: - cores: 3 bfast_wrapper: cores: 10 mem: 20