Mercurial > repos > rliterman > csp2
changeset 28:893a6993efe3
"planemo upload"
| author | rliterman |
|---|---|
| date | Wed, 04 Dec 2024 13:48:13 -0500 |
| parents | 792274118b2e |
| children | b6ec322b1f05 |
| files | CSP2/bin/chooseRefs.py CSP2/bin/fetchReads.py CSP2/bin/runSNPPipeline.py CSP2/bin/saveSNPDiffs.py CSP2/bin/screenSNPDiffs.py CSP2/bin/userSNPDiffs.py CSP2/conf/profiles.config CSP2/nextflow.config CSP2/subworkflows/fetchData/main.nf |
| diffstat | 9 files changed, 19 insertions(+), 14 deletions(-) [+] |
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--- a/CSP2/bin/chooseRefs.py Wed Dec 04 12:50:59 2024 -0500 +++ b/CSP2/bin/chooseRefs.py Wed Dec 04 13:48:13 2024 -0500 @@ -85,7 +85,7 @@ parser = argparse.ArgumentParser(description='Choose reference isolates based on FASTA metrics and mean distances.') parser.add_argument('--ref_count', type=int, default=1, help='Number of reference isolates to select') parser.add_argument('--mash_triangle_file', type=str, help='Path to the mash triangle file') -parser.add_argument('--trim_name', type=str, default="", help='trim name') +parser.add_argument('--trim_name', nargs='?', const="", default="", type=str, help='Trim name') args = parser.parse_args() ref_count = args.ref_count
--- a/CSP2/bin/fetchReads.py Wed Dec 04 12:50:59 2024 -0500 +++ b/CSP2/bin/fetchReads.py Wed Dec 04 13:48:13 2024 -0500 @@ -11,7 +11,7 @@ parser.add_argument('--read_filetype',default='fastq.gz', type=str, help='read filetype information') parser.add_argument('--forward_suffix',default='_1.fastq.gz', type=str, help='forward suffix') parser.add_argument('--reverse_suffix',default = '_2.fastq.gz', type=str, help='reverse suffix') -parser.add_argument('--trim_name', type=str, default="", help='trim name') +parser.add_argument('--trim_name', nargs='?', const="", default="", type=str, help='Trim name') args = parser.parse_args() # Get path to directory containing read files
--- a/CSP2/bin/runSNPPipeline.py Wed Dec 04 12:50:59 2024 -0500 +++ b/CSP2/bin/runSNPPipeline.py Wed Dec 04 13:48:13 2024 -0500 @@ -643,7 +643,7 @@ parser.add_argument('--query_edge', default=150,type=int, help='Query edge') parser.add_argument('--density_windows', default="1000,125,15",type=str, help='Density windows') parser.add_argument('--max_snps', default="3,2,1", type=str, help='Maximum SNPs') -parser.add_argument('--trim_name', type=str, default="", help='trim name') +parser.add_argument('--trim_name', nargs='?', const="", default="", type=str, help='Trim name') parser.add_argument('--max_missing',default=50, type=float, help='Maximum missing') parser.add_argument('--tmp_dir',default="", type=str, help='Temporary directory') parser.add_argument('--rescue', default="norescue",type=str, help='Rescue edge SNPs (rescue/norescue)')
--- a/CSP2/bin/saveSNPDiffs.py Wed Dec 04 12:50:59 2024 -0500 +++ b/CSP2/bin/saveSNPDiffs.py Wed Dec 04 13:48:13 2024 -0500 @@ -30,7 +30,7 @@ parser.add_argument("--snpdiffs_file", help="Path to the SNP diffs list file") parser.add_argument("--summary_file", help="Path to the summary file") parser.add_argument("--isolate_file", help="Path to the isolate data file") -parser.add_argument('--trim_name', type=str, default="", help='trim name') +parser.add_argument('--trim_name', nargs='?', const="", default="", type=str, help='Trim name') parser.add_argument("--ref_id_file", help="Path to the reference IDs file") args = parser.parse_args()
--- a/CSP2/bin/screenSNPDiffs.py Wed Dec 04 12:50:59 2024 -0500 +++ b/CSP2/bin/screenSNPDiffs.py Wed Dec 04 13:48:13 2024 -0500 @@ -555,7 +555,7 @@ parser.add_argument("--query_edge", default=150,type=int, help="Query edge") parser.add_argument("--density_windows",default="1000,125,15", help="Density windows (comma-separated)") parser.add_argument("--max_snps", default="3,2,1",help="Maximum SNPs (comma-separated)") -parser.add_argument('--trim_name', type=str, default="", help='trim name') +parser.add_argument('--trim_name', nargs='?', const="", default="", type=str, help='Trim name') parser.add_argument("--output_file", help="Output file") parser.add_argument("--ref_id", help="Reference IDs file") parser.add_argument("--tmp_dir",default="", help="TMP dir")
--- a/CSP2/bin/userSNPDiffs.py Wed Dec 04 12:50:59 2024 -0500 +++ b/CSP2/bin/userSNPDiffs.py Wed Dec 04 13:48:13 2024 -0500 @@ -31,7 +31,7 @@ parser = argparse.ArgumentParser() parser.add_argument("--snpdiffs_file", help="Path to the SNP diffs list file") -parser.add_argument('--trim_name', type=str, default="", help='trim name') +parser.add_argument('--trim_name', nargs='?', const="", default="", type=str, help='Trim name') args = parser.parse_args() snpdiffs_list_file = args.snpdiffs_file
--- a/CSP2/conf/profiles.config Wed Dec 04 12:50:59 2024 -0500 +++ b/CSP2/conf/profiles.config Wed Dec 04 13:48:13 2024 -0500 @@ -90,7 +90,7 @@ executor.$slurm.exitReadTimeout = 120000 process.executor = 'slurm' - params.cores = 8 + params.cores = 1 params.python_module = "" params.mummer_module = "" params.skesa_module = ""
--- a/CSP2/nextflow.config Wed Dec 04 12:50:59 2024 -0500 +++ b/CSP2/nextflow.config Wed Dec 04 13:48:13 2024 -0500 @@ -15,12 +15,14 @@ // CPU/memory settings process { withLabel: 'mummerMem' { + task_name = 'CSP2-MUMmer' cpus = 1 - // memory = '4 GB' + //memory = '4 GB' } - //withLabel: 'skesaMem' { - // memory = '12 GB' - //} + withLabel: 'skesaMem' { + task_name = 'CSP2-SKESA' + //memory = '12 GB' + } } // Global default params
--- a/CSP2/subworkflows/fetchData/main.nf Wed Dec 04 12:50:59 2024 -0500 +++ b/CSP2/subworkflows/fetchData/main.nf Wed Dec 04 13:48:13 2024 -0500 @@ -20,7 +20,8 @@ userSNPDiffs = file("${projectDir}/bin/userSNPDiffs.py") // Set SKESA cores to 4 or fewer -skesa_cpus = (params.cores as Integer) >= 4 ? 4 : params.cores as Integer +//skesa_cpus = (params.cores as Integer) >= 4 ? 4 : params.cores as Integer +skesa_cpus = 1 workflow { main: @@ -499,8 +500,10 @@ assembled_data = assembly_output.map{it->tuple(it[0],it[3])} } process skesaAssemble{ - //label 'skesaMem' - + label 'skesaMem' + + cpus = skesa_cpus + input: tuple val(sample_name),val(read_type),val(read_location)