Mercurial > repos > kkonganti > cfsan_centriflaken
changeset 58:2256bc31d3bf
"planemo upload"
| author | kkonganti |
|---|---|
| date | Wed, 13 Jul 2022 12:47:22 -0400 |
| parents | cea27772bcb8 |
| children | a8d6f5950fbf |
| files | cfsan_centriflaken.xml |
| diffstat | 1 files changed, 68 insertions(+), 43 deletions(-) [+] |
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--- a/cfsan_centriflaken.xml Tue Jul 12 16:56:17 2022 -0400 +++ b/cfsan_centriflaken.xml Wed Jul 13 12:47:22 2022 -0400 @@ -7,36 +7,46 @@ <version_command>nextflow -version</version_command> <command detect_errors="exit_code"><![CDATA[ mkdir -p cpipes-input || exit 1; - #for $key in $input.keys() - ln -sf '$input[$key]' './cpipes-input/$key'; - #end for - pwd_path=\$(pwd); + pwd_path=\$(pwd); + #import os + #if (str($input_read_type_cond.input_read_type) == "single_long"): + #for $key in $input_read_type_cond.input.keys() + ln -sf '$input_read_type_cond.input[$key]' './cpipes-input/$key'; + #end for + #elif (str($input_read_cond.input_read_type) == "paired"): + #for $key in $input_read_type_cond.input_pair.keys() + #set $read_R1 = os.path.basename($input_read_type_cond.input_pair[$key]['forward']) + #set $read_R2 = os.path.basename($input_read_type_cond.input_pair[$key]['reverse']) + ln -sf '$input_read_type_cond.input_pair[$key]['forward']' './cpipes-input/$read_R1'; + ln -sf '$input_read_type_cond.input_pair[$key]['reverse']' './cpipes-input/$read_R2'; + #end for + #endif $__tool_directory__/0.2.1/cpipes - --pipeline $pipeline - #if ($pipeline == "centriflaken"): + --pipeline $input_read_type_cond.pipeline + #if ($input_read_type_cond.pipeline_cond.pipeline == "centriflaken"): --fq_single_end true --flye_genome_size '${genome_size}' - #if ($long_read_platform == "nanopore_corr"): + #if ($input_read_type_cond.pipeline_cond.long_read_platform == "nanopore_corr"): --flye_nano_corr true --flye_nano_raw false - #elif ($long_read_platform == "nanopore_hq"): + #elif ($input_read_type_cond.pipeline_cond.long_read_platform == "nanopore_hq"): --flye_nano_hq true --flye_nano_raw false - #elif ($long_read_platform == "pacbio_raw"): + #elif ($input_read_type_cond.pipeline_cond.long_read_platform == "pacbio_raw"): --flye_pacbio_raw true --flye_nano_raw false - #elif ($long_read_platform == "pacbio_corr"): + #elif ($input_read_type_cond.pipeline_cond.long_read_platform == "pacbio_corr"): --flye_pacbio_corr true --flye_nano_raw false - #elif ($long_read_platform == "pacbio_hifi"): + #elif ($input_read_type_cond.pipeline_cond.long_read_platform == "pacbio_hifi"): --flye_pacbio_hifi true --flye_nano_raw false #end if - #elif ($pipeline == "centriflaken_hy"): - #if ($reads_lib_layout == "single"): + #elif ($input_read_type_cond.pipeline_cond.pipeline == "centriflaken_hy"): + #if (str($input_read_cond.input_read_type) == "single_long"): --fq_single_end true - #elif ($reads_lib_layout == "paired"): - --fq_single_end false --fq2_suffix '${fq2_suffix}' + #elif (str($input_read_cond.input_read_type) == "paired"): + --fq_single_end false --fq2_suffix '${input_read_cond.fq2_suffix}' #end if #end if --input \${pwd_path}/cpipes-input --output \${pwd_path}/cpipes-output - --fq_suffix '${fq_suffix}' + --fq_suffix '${input_read_cond.fq_suffix}' #if ($fq_filter_by_len != ""): --fq_filter_by_len $fq_filter_by_len #end if @@ -44,35 +54,50 @@ --fq_filename_delim_idx $fq_filename_delim_idx --centrifuge_extract_bug '${centrifuge_extract_bug}' -profile kondagac; - mv './cpipes-output/${pipeline}-multiqc/multiqc_report.html' './multiqc_report.html'; - mv './cpipes-output/${pipeline}-results/kraken2_extract_contigs' kraken2_extract_contigs; - rm -rf ./cpipes-output; - rm -rf ./work + mv './cpipes-output/${pipeline}-multiqc/multiqc_report.html' './multiqc_report.html' || exit 1; + mv './cpipes-output/${pipeline}-results/kraken2_extract_contigs' kraken2_extract_contigs || exit 1; + rm -rf ./cpipes-output || exit 1; + rm -rf ./work || exit 1 ]]></command> <inputs> - <param name="input" type="data_collection" collection_type="list" format="fastq,fastq.gz,fastqsanger.gz,fastqsanger" label="Input read collection" /> - <param name="pipeline" type="select" label="CPIPES Workflow name" - help="centriflaken: for long reads (Nanopore or PacBio). centriflaken_hy: for short reads (paired or unpaired). Default: centriflaken"> - <option value="centriflaken" selected="true">centriflaken</option> - <option value="centriflaken_hy">centriflaken_hy</option> - </param> - <param name="reads_lib_layout" type="select" label="Short Read Library Layout" - help="Leave this option as Single-End for centriflaken. If the pipeline is centriflaken_hy (i.e for short reads), what is the library layout? Default: Single-End"> - <option value="single" selected="true">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" - help="THIS OPTION IS IGNORED IF THE INPUT READS ARE SHORT READS."> - <option value="nanopore_raw" selected="true">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" - help="THIS OPTION IS IGNORED IF THE INPUT READS ARE UNPAIRED/LONG READS."/> + <conditional name="input_read_type_cond"> + <param name="input_read_type" type="select" label="Select the read collection type"> + <option value="single_long" selected="true">Unpaired reads (i.e. Single-End short reads/Long reads)</option> + <option value="paired">Paired-End reads</option> + </param> + <when value="single_long"> + <param name="input" type="data_collection" collection_type="list" format="fastq,fastq.gz,fastqsanger.gz,fastqsanger" + label="Dataset list of unpaired short reads / long reads" /> + <conditional name="pipeline_cond"> + <param name="pipeline" type="select" label="CPIPES Workflow name" + help="centriflaken: for long reads (Nanopore or PacBio). centriflaken_hy: for short reads (paired or unpaired). Default: centriflaken"> + <option value="centriflaken" selected="true">centriflaken</option> + <option value="centriflaken_hy">centriflaken_hy</option> + </param> + <when value="centriflaken"> + <param name="long_read_platform" type="select" label="Mention long read sequencing platform and type"> + <option value="nanopore_raw" selected="true">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> + </when> + <when value="centriflaken_hy"> + <param name="long_read_platform" value="N/A" type="text" optional="true" label="Mention long read sequencing platform and type" + help="THIS OPTION IS IGNORED IF THE INPUT READS ARE SHORT READS."/> + </when> + </conditional> + <param name="fq_suffix" value=".fastq.gz" type="text" label="Suffix of the R1 FASTQ or Unpaired FASTQ"/> + </when> + <when value="paired"> + <param name="input_pair" type="data_collection" collection_type="list:paired" format="fastq,fastq.gz,fastqsanger.gz,fastqsanger" + label="List of Dataset pairs" /> + <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"/> + </when> + </conditional> <param name="fq_filter_by_len" optional="true" value="" type="integer" label="Enter minimum read length to retain before starting the analysis" help="Keep this option empty to use default values. Default for centriflaken (long reads) is 4000 bp and for centriflaken_hy (short reads) is 75 bp."/> <param name="fq_filename_delim" type="text" value="_" label="File name delimitor by which samples are grouped together (--fq_filename_delim)"