# HG changeset patch # User kkonganti # Date 1659107467 14400 # Node ID 8d7f482c64de7282768d6f33b56800ecf6b9010e # Parent ef0b422978fd0c96f8bab951485e1c08f1bf8c0f "planemo upload" diff -r ef0b422978fd -r 8d7f482c64de 0.3.0/README.md --- a/0.3.0/README.md Mon Jul 25 12:57:06 2022 -0400 +++ b/0.3.0/README.md Fri Jul 29 11:11:07 2022 -0400 @@ -20,7 +20,7 @@ Following is the example of how to run the `centriflaken` pipeline on the **CFSAN** raven cluster. ```bash -module load cpipes/0.2.1 +module load cpipes/0.3.0 cpipes --pipeline centriflaken [options] ``` diff -r ef0b422978fd -r 8d7f482c64de 0.3.0/lib/help/megahit.nf --- a/0.3.0/lib/help/megahit.nf Mon Jul 25 12:57:06 2022 -0400 +++ b/0.3.0/lib/help/megahit.nf Fri Jul 29 11:11:07 2022 -0400 @@ -8,6 +8,12 @@ tool.helpparams = [:] toolspecs = [ + 'megahit_run': [ + clihelp: 'Run MEGAHIT assembler. Default: ' + + (params.megahit_run ?: false), + cliflag: null, + clivalue: null + ], 'megahit_min_count': [ clihelp: '. Minimum multiplicity for filtering (k_min+1)-mers. ' + "Defaut: ${params.megahit_min_count}", diff -r ef0b422978fd -r 8d7f482c64de 0.3.0/lib/help/spades.nf --- a/0.3.0/lib/help/spades.nf Mon Jul 25 12:57:06 2022 -0400 +++ b/0.3.0/lib/help/spades.nf Fri Jul 29 11:11:07 2022 -0400 @@ -8,6 +8,12 @@ tool.helpparams = [:] toolspecs = [ + 'spades_run': [ + clihelp: 'Run SPAdes assembler. Default: ' + + (params.spades_run ?: false), + cliflag: null, + clivalue: null + ], 'spades_isolate': [ clihelp: 'This flag is highly recommended for high-coverage isolate and ' + "multi-cell data. Defaut: ${params.spades_isolate}", diff -r ef0b422978fd -r 8d7f482c64de 0.3.0/modules/megahit/assemble/main.nf --- a/0.3.0/modules/megahit/assemble/main.nf Mon Jul 25 12:57:06 2022 -0400 +++ b/0.3.0/modules/megahit/assemble/main.nf Fri Jul 29 11:11:07 2022 -0400 @@ -1,6 +1,6 @@ process MEGAHIT_ASSEMBLE { tag "$meta.id" - label 'process_high' + label 'process_higher' module (params.enable_module ? "${params.swmodulepath}${params.fs}megahit${params.fs}1.2.9" : null) conda (params.enable_conda ? "bioconda::megahit=1.2.9" : null) @@ -54,4 +54,4 @@ END_VERSIONS """ } -} \ No newline at end of file +} diff -r ef0b422978fd -r 8d7f482c64de 0.3.0/modules/multiqc/main.nf --- a/0.3.0/modules/multiqc/main.nf Mon Jul 25 12:57:06 2022 -0400 +++ b/0.3.0/modules/multiqc/main.nf Fri Jul 29 11:11:07 2022 -0400 @@ -15,7 +15,7 @@ path "*multiqc*" path "*multiqc_report.html", emit: report path "*_data" , emit: data - path "*_plots" , optional:true, emit: plots + path "*_plots" , optional: true, emit: plots path "versions.yml" , emit: versions when: diff -r ef0b422978fd -r 8d7f482c64de 0.3.0/modules/spades/assemble/main.nf --- a/0.3.0/modules/spades/assemble/main.nf Mon Jul 25 12:57:06 2022 -0400 +++ b/0.3.0/modules/spades/assemble/main.nf Fri Jul 29 11:11:07 2022 -0400 @@ -1,6 +1,6 @@ process SPADES_ASSEMBLE { tag "$meta.id" - label 'process_high' + label 'process_higher' module (params.enable_module ? "${params.swmodulepath}${params.fs}spades${params.fs}3.15.3" : null) conda (params.enable_conda ? 'bioconda::spades=3.15.3' : null) diff -r ef0b422978fd -r 8d7f482c64de 0.3.0/nextflow.config --- a/0.3.0/nextflow.config Mon Jul 25 12:57:06 2022 -0400 +++ b/0.3.0/nextflow.config Fri Jul 29 11:11:07 2022 -0400 @@ -27,8 +27,8 @@ includeConfig "${pd}${fs}conf${fs}modules.config" // Nextflow runtime profiles -conda.cacheDir = '/tool/tool-data/cfsan-centriflaken-db/0/kondagac_cache' -singularity.cacheDir = '/tool/tool-data/cfsan-centriflaken-db/0/cingularitygac_cache' +conda.cacheDir = '/tool-local-data/cfsan-centriflaken-db/0/kondagac_cache' +singularity.cacheDir = '/tool-local-data/cfsan-centriflaken-db/0/cingularitygac_cache' profiles { standard { diff -r ef0b422978fd -r 8d7f482c64de 0.3.0/readme/centriflaken.md --- a/0.3.0/readme/centriflaken.md Mon Jul 25 12:57:06 2022 -0400 +++ b/0.3.0/readme/centriflaken.md Fri Jul 29 11:11:07 2022 -0400 @@ -15,7 +15,7 @@ #### Workflow Usage ```bash -module load cpipes/0.2.1 +module load cpipes/0.3.0 cpipes --pipeline centriflaken [options] ``` diff -r ef0b422978fd -r 8d7f482c64de 0.3.0/readme/centriflaken_hy.md --- a/0.3.0/readme/centriflaken_hy.md Mon Jul 25 12:57:06 2022 -0400 +++ b/0.3.0/readme/centriflaken_hy.md Fri Jul 29 11:11:07 2022 -0400 @@ -15,7 +15,7 @@ #### Workflow Usage ```bash -module load cpipes/0.2.1 +module load cpipes/0.3.0 cpipes --pipeline centriflaken_hy [options] ``` @@ -43,7 +43,7 @@ ```text [Kranti.Konganti@login2-slurm ]$ cpipes --pipeline centriflaken_hy --help N E X T F L O W ~ version 21.12.1-edge -Launching `/nfs/software/apps/cpipes/0.2.1/cpipes` [wise_noyce] - revision: 72db279311 +Launching `/home/Kranti.Konganti/apps/cpipes/cpipes` [condescending_jang] - revision: 72db279311 ================================================================================ (o) ___ _ __ _ _ __ ___ ___ @@ -57,7 +57,7 @@ -------------------------------------------------------------------------------- Name : CPIPES Author : Kranti.Konganti@fda.hhs.gov -Version : 0.2.1 +Version : 0.3.0 Center : CFSAN, FDA. ================================================================================ @@ -65,7 +65,7 @@ Author : Kranti.Konganti@fda.hhs.gov -Version : 0.2.0 +Version : 0.3.0 Usage : cpipes --pipeline centriflaken_hy [options] @@ -176,6 +176,59 @@ --centrifuge_ignore_quals : Treat all quality values as 30 on Phred scale. Default: false +--megahit_run : Run MEGAHIT assembler. Default: true + +--megahit_min_count : . Minimum multiplicity for filtering ( + k_min+1)-mers. Defaut: false + +--megahit_k_list : Comma-separated list of kmer size. All + values must be odd, in the range 15-255, + increment should be <= 28. Ex: '21,29,39,59, + 79,99,119,141'. Default: false + +--megahit_no_mercy : Do not add mercy k-mers. Default: false + +--megahit_bubble_level : . Intensity of bubble merging (0-2), 0 + to disable. Default: false + +--megahit_merge_level : . Merge complex bubbles of length <= l* + kmer_size and similarity >= s. Default: + false + +--megahit_prune_level : . Strength of low depth pruning (0-3). + Default: false + +--megahit_prune_depth : . Remove unitigs with avg k-mer depth + less than this value. Default: false + +--megahit_low_local_ratio : . Ratio threshold to define low + local coverage contigs. Default: false + +--megahit_max_tip_len : . remove tips less than this value [< + int> * k]. Default: false + +--megahit_no_local : Disable local assembly. Default: false + +--megahit_kmin_1pass : Use 1pass mode to build SdBG of k_min. + Default: false + +--megahit_preset : . Override a group of parameters. + Valid values are meta-sensitive which + enforces '--min-count 1 --k-list 21,29,39, + 49,...,129,141', meta-large (large & + complex metagenomes, like soil) which + enforces '--k-min 27 --k-max 127 --k-step + 10'. Default: meta-sensitive + +--megahit_mem_flag : . SdBG builder memory mode. 0: minimum; + 1: moderate; 2: use all memory specified. + Default: 2 + +--megahit_min_contig_len : . Minimum length of contigs to output. + Default: false + +--spades_run : Run SPAdes assembler. Default: false + --spades_isolate : This flag is highly recommended for high- coverage isolate and multi-cell data. Defaut: false @@ -212,7 +265,7 @@ Default: false --spades_only_assembler : Runs only the SPAdes assembler module ( - without read error correction).Default: + without read error correction). Default: false --spades_careful : Tries to reduce the number of mismatches diff -r ef0b422978fd -r 8d7f482c64de 0.3.0/workflows/conf/centriflaken.config --- a/0.3.0/workflows/conf/centriflaken.config Mon Jul 25 12:57:06 2022 -0400 +++ b/0.3.0/workflows/conf/centriflaken.config Fri Jul 29 11:11:07 2022 -0400 @@ -2,13 +2,13 @@ workflow_blueprint_by = 'Narjol.Gonzalez-Escalona@fda.hhs.gov' workflow_built_by = 'Kranti.Konganti@fda.hhs.gov' workflow_version = '0.2.0' - centrifuge_x = '/tool/tool-data/cfsan-centriflaken-db/0/centrifuge/2022-04-12/ab' + centrifuge_x = '/tool-local-data/cfsan-centriflaken-db/0/centrifuge/2022-04-12/ab' centrifuge_extract_bug = 'Escherichia coli' centrifuge_save_aligned = false centrifuge_save_unaligned = false centrifuge_out_fmt_sam = false centrifuge_ignore_quals = false - kraken2_db = '/tool/tool-data/cfsan-centriflaken-db/0/kraken2/standard-210914' + kraken2_db = '/tool-local-data/cfsan-centriflaken-db/0/kraken2/standard-210914' kraken2_confidence = '0.0' kraken2_quick = false kraken2_use_mpa_style = false @@ -34,7 +34,7 @@ ectyper_perc_opcov = 95 ectyper_perc_hpcov = 50 serotypefinder_run = (params.centrifuge_extract_bug ==~ /(?i)Salmonella/ ? false : true) - serotypefinder_db = '/tool/tool-data/cfsan-centriflaken-db/0/serotypefinder/2.0.2' + serotypefinder_db = '/tool-local-data/cfsan-centriflaken-db/0/serotypefinder/2.0.2' serotypefinder_min_cov = 0.80 serotypefinder_min_threshold = 0.85 serotypefinder_x = true @@ -48,10 +48,10 @@ mlst_mincov = 10 mlst_minscore = 50 amrfinderplus_run = false - amrfinderplus_db = '/tool/tool-data/cfsan-centriflaken-db/0/amrfinderplus/3.10.24/latest' + amrfinderplus_db = '/tool-local-data/cfsan-centriflaken-db/0/amrfinderplus/3.10.24/latest' amrfinderplus_genes = true abricate_run = true - abricate_datadir = '/tool/tool-data/cfsan-centriflaken-db/0/abricate/1.0.1/db' + abricate_datadir = '/tool-local-data/cfsan-centriflaken-db/0/abricate/1.0.1/db' abricate_minid = 90 abricate_mincov = 80 abricate_summary_run = true diff -r ef0b422978fd -r 8d7f482c64de 0.3.0/workflows/conf/centriflaken_hy.config --- a/0.3.0/workflows/conf/centriflaken_hy.config Mon Jul 25 12:57:06 2022 -0400 +++ b/0.3.0/workflows/conf/centriflaken_hy.config Fri Jul 29 11:11:07 2022 -0400 @@ -2,13 +2,13 @@ workflow_blueprint_by = 'Narjol.Gonzalez-Escalona@fda.hhs.gov' workflow_built_by = 'Kranti.Konganti@fda.hhs.gov' workflow_version = '0.3.0' - centrifuge_x = '/tool/tool-data/cfsan-centriflaken-db/0/centrifuge/2022-04-12/ab' + centrifuge_x = '/tool-local-data/cfsan-centriflaken-db/0/centrifuge/2022-04-12/ab' centrifuge_extract_bug = 'Escherichia coli' centrifuge_save_aligned = false centrifuge_save_unaligned = false centrifuge_out_fmt_sam = false centrifuge_ignore_quals = false - kraken2_db = '/tool/tool-data/cfsan-centriflaken-db/0/kraken2/standard-210914' + kraken2_db = '/tool-local-data/cfsan-centriflaken-db/0/kraken2/standard-210914' kraken2_confidence = '0.0' kraken2_quick = false kraken2_use_mpa_style = false @@ -55,7 +55,7 @@ ectyper_perc_opcov = 95 ectyper_perc_hpcov = 50 serotypefinder_run = (params.centrifuge_extract_bug ==~ /(?i)Salmonella/ ? false : true) - serotypefinder_db = '/tool/tool-data/cfsan-centriflaken-db/0/serotypefinder/2.0.2' + serotypefinder_db = '/tool-local-data/cfsan-centriflaken-db/0/serotypefinder/2.0.2' serotypefinder_min_cov = 0.80 serotypefinder_min_threshold = 0.85 serotypefinder_x = true @@ -69,10 +69,10 @@ mlst_mincov = 10 mlst_minscore = 50 amrfinderplus_run = false - amrfinderplus_db = '/tool/tool-data/cfsan-centriflaken-db/0/amrfinderplus/3.10.24/latest' + amrfinderplus_db = '/tool-local-data/cfsan-centriflaken-db/0/amrfinderplus/3.10.24/latest' amrfinderplus_genes = true abricate_run = true - abricate_datadir = '/tool/tool-data/cfsan-centriflaken-db/0/abricate/1.0.1/db' + abricate_datadir = '/tool-local-data/cfsan-centriflaken-db/0/abricate/1.0.1/db' abricate_minid = 90 abricate_mincov = 80 abricate_summary_run = true