Mercurial > repos > kkonganti > cfsan_centriflaken
changeset 25:b9cd7722d51b
"planemo upload"
| author | kkonganti |
|---|---|
| date | Wed, 29 Jun 2022 12:45:02 -0400 |
| parents | 05b6b4edfd58 |
| children | 2fb6c7a719d4 |
| files | 0.2.1/conf/modules.config cfsan_centriflaken.xml |
| diffstat | 2 files changed, 22 insertions(+), 2 deletions(-) [+] |
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--- a/0.2.1/conf/modules.config Wed Jun 29 09:47:38 2022 -0400 +++ b/0.2.1/conf/modules.config Wed Jun 29 12:45:02 2022 -0400 @@ -11,10 +11,10 @@ ] errorStrategy = { - ![0].contains(task.exitStatus) ? dynamic_retry(task.attempt, 1000) : 'finish' + ![0].contains(task.exitStatus) ? dynamic_retry(task.attempt, 10) : 'finish' } - maxRetries = 11 + maxRetries = 21 withLabel: 'process_femto' { cpus = 2
--- a/cfsan_centriflaken.xml Wed Jun 29 09:47:38 2022 -0400 +++ b/cfsan_centriflaken.xml Wed Jun 29 12:45:02 2022 -0400 @@ -30,6 +30,17 @@ --fq_filename_delim_idx $fq_filename_delim_idx --centrifuge_extract_bug '${centrifuge_extract_bug}' --flye_genome_size '${genome_size}' + #if ($long_read_platform == "nanopore_corr"): + --flye_nano_corr true --flye_nano_raw false + #elif ($long_read_platform == "nanopore_hq"): + --flye_nano_hq true --flye_nano_raw false + #elif ($long_read_platform == "pacbio_raw"): + --flye_pacbio_raw true --flye_nano_raw false + #elif ($long_read_platform == "pacbio_corr"): + --flye_pacbio_corr true --flye_nano_raw false + #elif ($long_read_platform == "pacbio_hifi"): + --flye_pacbio_hifi true --flye_nano_raw false + #end if -profile $runtime_profile -resume; mv './cpipes-output/${pipeline}-multiqc/multiqc_report.html' './multiqc_report.html'; @@ -47,6 +58,15 @@ <option value="single">Single-End</option> <option value="paired">Paired-End</option> </param> + <param name="long_read_platform" type="select" label="Mention long read sequencing platform and type" value="nanopore_raw" + help="THIS OPTION IS IGNORED IF THE INPUT READS ARE SHORT READS."> + <option value="nanopore_raw">Nanopore raw reads, pre-Guppy5 (<20% error)</option> + <option value="nanopore_corr">Nanopore reads that were corrected with other methods (<3% error)</option> + <option value="nanopore_hq">Nanopore high-quality reads, Guppy5+ SUP or Q20 (5% error)</option> + <option value="pacbio_raw">PacBio regular CLR reads (<20% error)</option> + <option value="pacbio_corr">PacBio reads that were corrected with other methods (<3% error)</option> + <option value="pacbio_hifi">PacBio HiFi reads (<1% error)</option> + </param> <param name="fq_suffix" value=".fastq.gz" type="text" label="Suffix of the R1 FASTQ or Unpaired FASTQ"/> <param name="fq2_suffix" value="_R2_001.fastq.gz" type="text" label="Suffix of the R2 FASTQ R2"/> <param name="fq_filename_delim" type="text" value="_" label="File name delimitor by which samples are grouped together (--fq_filename_delim)"