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updated log, readme and help
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MarieLataretu authored May 22, 2024
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2 changes: 1 addition & 1 deletion README.md
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Expand Up @@ -206,7 +206,7 @@ Sample_2021,barcode01,good
* poreCov was coded with "easy to use" in mind, while staying flexible
* therefore we provide a few input types which adjusts the workflow automatically (see image below)
* fast5 raw data, fastq files (one sample per file), fastq_pass (the basecalling output) or fasta (supports multifastas)
* primer schemes for ARTIC can be V1, V2, V3(default), V4, V4.1 or V1200 (the 1200bp amplicon ones)
* primer schemes for ARTIC can be V1, V2, V3(default), V4, V4.1 (the 400bp amplicon ones), V1200 or V5.2.0_1200 (the 1200bp amplicon ones)

<p align="left">
<img src="data/figures/workflow.png" width="700" title="Workflow">
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6 changes: 3 additions & 3 deletions poreCov.nf
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Expand Up @@ -509,11 +509,11 @@ ${c_yellow}Parameters - SARS-CoV-2 genome reconstruction (optional)${c_reset}
--primerV Supported primer variants or primer bed files - choose one [default: ${params.primerV}]
${c_dim}ARTIC:${c_reset} V1, V2, V3, V4, V4.1, V.5, V.5.1, V.5.3.2_400
${c_dim}NEB:${c_reset} VarSkipV1a, VarSkipV2, VarSkipV2b
${c_dim}Other:${c_reset} V1200 ${c_dim}(also known as midnight)${c_reset}
${c_dim}Other:${c_reset} V1200, V5.2.0_1200 ${c_dim}(also known as midnight)${c_reset}
${c_dim}Primer bed file:${c_reset} e.g. primers.bed ${c_dim}See Readme for more help${c_reset}
--rapid rapid-barcoding-kit was used [default: ${params.rapid}]
--minLength min length filter raw reads [default: 100]
--maxLength max length filter raw reads [default: 700 (primer-scheme: V1-4, rapid); 1500 (primer-scheme: V1200)]
--maxLength max length filter raw reads [default: 700 (primer-scheme: V1-4, rapid); 1500 (primer-scheme: V1200, V5.2.0_1200)]
--min_depth nucleotides below min depth will be masked to "N" [default ${params.min_depth}]
--medaka_model medaka model for the artic workflow [default: ${params.medaka_model}]
e.g. "r941_min_hac_g507" or "r941_min_sup_g507"
Expand Down Expand Up @@ -620,7 +620,7 @@ def read_length() {
log_msg_read_min_length = params.minLength
log_msg_read_max_length = params.maxLength

if ( params.primerV.matches('V1200')) {
if ( params.primerV.matches('V1200') || params.primerV.matches('V5.2.0_1200') ) {
if ( !params.minLength ) { log_msg_read_min_length = 400 }
if ( !params.maxLength ) { log_msg_read_max_length = 1500 }
}
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