Vfnext bdotto #18
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Vfnext bdotto #18
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bdotto82
reviewed
Oct 31, 2022
bdotto82
approved these changes
Oct 31, 2022
AMarinhoSN
approved these changes
Nov 3, 2022
dezordi
added a commit
that referenced
this pull request
Sep 6, 2023
* [add] bwa index proc * [add] fastp proc * [add] nextflow config * [add] align2ref proc * [add] main * [add] modular containers recipes and run on containers by default * [upd] files to be ignored by git * [add] Ivar to workflow * [add] read counts to workflow * [add] align consensus sequence 2 ref * [add] new steps * [add] run intrahost script * [add] intrahost container recipe and files * [add] run pangolin * [add] run nextclade * [add] run Picard * [add] fix WGS * [fix] include fixWGS module * [add] setup containers bash script * [add] publish results on output dir * [add] README * [fix] usable arbitrary paths for fastqs, reference and adapters files * Add new function of intrahost_script * change regions to region * [upd] intrahost analyses to handle gff * [add] reference gff on the test_files dir * [fix] missing mutation data on publishDir (temporary fix) * [add] script to compile outputs * remove unused channel * [add] vfnext flowchart * [add] compile output step * [fix] missing compile outputs include * [add] input handling and parameters validation * [enh] a separate config file * [add] process to get ref .gff and .fa * [add] gff for intrahostcript * [add] ignore ref fasta and gff provided if a valid virus tag is set * [fix] adapt process to new reference fasta behaviour * [add] container recipe for NCBI edirect tools * [fix] ignoring fa and gff, only if a valid AND not "custom" tag is set * [add] snpeff container * [add] module to generate faidx * [add] module to generate vcfs * [fix] add check for refGenomeCode for custom virus * [fix] modules who someone (totally not me) forgot to include * [add] optionally run SnpEff * [enh] check for fq.gz or fastq.gz and raise an error if channel is empty * [fix] individual virus final trigger for compileOutputs * Update README.md * put compile output only for sars-cov-2 (temporary) * Update README.md * update gff tretament to work with genbank gff too * remove comments from main * [fix] snpeff container as a sandbox, to allow to write db inside it * [enh] if refGenomeCode is specified, no gff and fa is required * [upd] nextclade usage and set it to version 2.4.0 instead of latest * [add] optional behaviour for adapters file * [enh] do not break pipeline if runSNPeff fails * fix nextclade filename * add container to align2ref * [add] compiled at results base dir, fix minor bug * run SnpEff unless required to do not do so * [add] write mapped reads fq files * [add] set container for getMappedReads * [enh] empty seq error handling for fixWGS * [fix] error handling for no data to compile * [add] read counts to compileOutput * add metrics files to fixWGS input * remove legacy code * [add] write unmmaped reads as fq files * [fix] add COMPILED_OUTPUT dir (+ minor fixes) * [add] param to deactivate run for writeMappedReads * [add] compile output for custom virus * [fix] compileOutput for sars-cov2 * add snpEff stats outputs and mapping of fastp.html output * [fix] compile output for custom * [add] check for genome code at snpeff database * [add] get html reports via vfreport * fix ref_gcode at line 125 * move vfreport output to COMPILED_OUTPUT dir * new handling of cpus/threads resources * add lineage and short summary * change short summary column names and breadth coverage decimals * chenge test files structure * add wrapper CLI * Update README.rst added new wrapper CLI instructions * fix setup and test.params * add new entries to snpeff db * add singlethread label * add denv test files * update snpeff db catalog after new entry added * fix snpEffectPredictor bug (needs to run as sudo) * do not download fasta file if custom virus * add runSnpEff on denv.params * Create README.md * add .bai to output * set output files and do not publish symlinks * fix .bai publish * Vfnext bdotto (#18) * Ajustes para rodar sem root * Alteração setup * Ajustes setup * Ajustes setup * Picrd Container * add env.yml * Delete .nextflow.log.1 Co-authored-by: Bruno Dotto <[email protected]> Co-authored-by: Antonio Marinho <[email protected]> * update main.nf and runReadCounts.nf to recognize reference genome as input * add update pangolin container via CLI * add fiocruz hpc profiles * use nextflowSimCalls only for standard profile * fix fiocruz profiles * increase cpus for fiocruz_standard * fix maxcpus error * Update README.rst * Update env.yml * Delete viralflow.yml * Delete images directory * Vfnext quality params (#20) * add mapping and base quality params * add quality params do wrapper * add mp and bq to runsnpeff * add pango update data option (#21) * add writable option to container * handle missing files without breaking the pipeline * fix short_summary bug * fix missing short_summary for custom * remove threads param from log.info * fix ivar container * remove empty files from fastq channel * minor fixes * add samtools ampliconclip function * fix adapters_file logic * update warn reference from fastp to samtools * change name of 'adaptersFile' to 'primersBED' * rename adaptersFile to primersBED * add optional output of timmed_reads.txt * correction of params file for SC2 * set fastp fq.gz as input for align2ref * fix unmapped reads from fastq * set prefix as sample_id * fix coverage breadth colum in short_summary for custom mode * fix debian repositories in bwa and fastp recipes * standardize custom short summary cols names * add bam filtering by size (for picard input) * consistent identation * feed filtered ch to picard (facepalm) * add warning if empty fastqs were found * Update denv.params Update of default depth parameter to 25. * Update sars-cov-2.params Update of default depth parameter to 25. * Update README.md * update ivar container * fix bam filter bug for no bed file * break cmd into multiple lines * fix picard missing input * Update README.rst Co-authored-by: dezordi <[email protected]> * Update vfnext/README.md Co-authored-by: dezordi <[email protected]> * update version * update version number * update * update * update readme * specify what was borrowed from nxf-fastqc * update wrapper * update version * Update README.rst Co-authored-by: alexandrefreitasdasilva <92752518+alexandrefreitasdasilva@users.noreply.github.com> * Update vfnext/README.md Co-authored-by: alexandrefreitasdasilva <92752518+alexandrefreitasdasilva@users.noreply.github.com> * Update vfnext/README.md Co-authored-by: alexandrefreitasdasilva <92752518+alexandrefreitasdasilva@users.noreply.github.com> * Update vfnext/workflows/step0-input-handling.nf Co-authored-by: alexandrefreitasdasilva <92752518+alexandrefreitasdasilva@users.noreply.github.com> * Update vfnext/workflows/step0-input-handling.nf Co-authored-by: alexandrefreitasdasilva <92752518+alexandrefreitasdasilva@users.noreply.github.com> * print VF version on wrapper * depth param default changed from 5 to 25 --------- Co-authored-by: dezordi <[email protected]> Co-authored-by: Bruno Dotto <[email protected]> Co-authored-by: bdotto82 <[email protected]> Co-authored-by: alexandrefreitasdasilva <[email protected]> Co-authored-by: alexandrefreitasdasilva <92752518+alexandrefreitasdasilva@users.noreply.github.com>
dezordi
added a commit
that referenced
this pull request
Sep 23, 2023
* [add] bwa index proc * [add] fastp proc * [add] nextflow config * [add] align2ref proc * [add] main * [add] modular containers recipes and run on containers by default * [upd] files to be ignored by git * [add] Ivar to workflow * [add] read counts to workflow * [add] align consensus sequence 2 ref * [add] new steps * [add] run intrahost script * [add] intrahost container recipe and files * [add] run pangolin * [add] run nextclade * [add] run Picard * [add] fix WGS * [fix] include fixWGS module * [add] setup containers bash script * [add] publish results on output dir * [add] README * [fix] usable arbitrary paths for fastqs, reference and adapters files * Add new function of intrahost_script * change regions to region * [upd] intrahost analyses to handle gff * [add] reference gff on the test_files dir * [fix] missing mutation data on publishDir (temporary fix) * [add] script to compile outputs * remove unused channel * [add] vfnext flowchart * [add] compile output step * [fix] missing compile outputs include * [add] input handling and parameters validation * [enh] a separate config file * [add] process to get ref .gff and .fa * [add] gff for intrahostcript * [add] ignore ref fasta and gff provided if a valid virus tag is set * [fix] adapt process to new reference fasta behaviour * [add] container recipe for NCBI edirect tools * [fix] ignoring fa and gff, only if a valid AND not "custom" tag is set * [add] snpeff container * [add] module to generate faidx * [add] module to generate vcfs * [fix] add check for refGenomeCode for custom virus * [fix] modules who someone (totally not me) forgot to include * [add] optionally run SnpEff * [enh] check for fq.gz or fastq.gz and raise an error if channel is empty * [fix] individual virus final trigger for compileOutputs * Update README.md * put compile output only for sars-cov-2 (temporary) * Update README.md * update gff tretament to work with genbank gff too * remove comments from main * [fix] snpeff container as a sandbox, to allow to write db inside it * [enh] if refGenomeCode is specified, no gff and fa is required * [upd] nextclade usage and set it to version 2.4.0 instead of latest * [add] optional behaviour for adapters file * [enh] do not break pipeline if runSNPeff fails * fix nextclade filename * add container to align2ref * [add] compiled at results base dir, fix minor bug * run SnpEff unless required to do not do so * [add] write mapped reads fq files * [add] set container for getMappedReads * [enh] empty seq error handling for fixWGS * [fix] error handling for no data to compile * [add] read counts to compileOutput * add metrics files to fixWGS input * remove legacy code * [add] write unmmaped reads as fq files * [fix] add COMPILED_OUTPUT dir (+ minor fixes) * [add] param to deactivate run for writeMappedReads * [add] compile output for custom virus * [fix] compileOutput for sars-cov2 * add snpEff stats outputs and mapping of fastp.html output * [fix] compile output for custom * [add] check for genome code at snpeff database * [add] get html reports via vfreport * fix ref_gcode at line 125 * move vfreport output to COMPILED_OUTPUT dir * new handling of cpus/threads resources * add lineage and short summary * change short summary column names and breadth coverage decimals * chenge test files structure * add wrapper CLI * Update README.rst added new wrapper CLI instructions * fix setup and test.params * add new entries to snpeff db * add singlethread label * add denv test files * update snpeff db catalog after new entry added * fix snpEffectPredictor bug (needs to run as sudo) * do not download fasta file if custom virus * add runSnpEff on denv.params * Create README.md * add .bai to output * set output files and do not publish symlinks * fix .bai publish * Vfnext bdotto (#18) * Ajustes para rodar sem root * Alteração setup * Ajustes setup * Ajustes setup * Picrd Container * add env.yml * Delete .nextflow.log.1 Co-authored-by: Bruno Dotto <[email protected]> Co-authored-by: Antonio Marinho <[email protected]> * update main.nf and runReadCounts.nf to recognize reference genome as input * add update pangolin container via CLI * add fiocruz hpc profiles * use nextflowSimCalls only for standard profile * fix fiocruz profiles * increase cpus for fiocruz_standard * fix maxcpus error * Update README.rst * Update env.yml * Delete viralflow.yml * Delete images directory * Vfnext quality params (#20) * add mapping and base quality params * add quality params do wrapper * add mp and bq to runsnpeff * add pango update data option (#21) * add writable option to container * handle missing files without breaking the pipeline * fix short_summary bug * fix missing short_summary for custom * remove threads param from log.info * fix ivar container * remove empty files from fastq channel * minor fixes * add samtools ampliconclip function * fix adapters_file logic * update warn reference from fastp to samtools * change name of 'adaptersFile' to 'primersBED' * rename adaptersFile to primersBED * add optional output of timmed_reads.txt * correction of params file for SC2 * set fastp fq.gz as input for align2ref * fix unmapped reads from fastq * set prefix as sample_id * fix coverage breadth colum in short_summary for custom mode * fix debian repositories in bwa and fastp recipes * standardize custom short summary cols names * add documment template * remove version * update template * remove yaml * add usage * add initial usage info * add basic usage and start tasks * add img, and tasks * Update README.md * Update README.md * Update README.md * Update Singularity_ivar * Update Singularity_ivar * Update README.rst * Update README.rst * Delete wrapper/viralflow_dev * remove _dev information --------- Co-authored-by: AMarinhoSN <[email protected]> Co-authored-by: Antonio Marinho <[email protected]> Co-authored-by: Bruno Dotto <[email protected]> Co-authored-by: bdotto82 <[email protected]> Co-authored-by: alexandrefreitasdasilva <[email protected]> Co-authored-by: dezordi <[email protected]>
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A ideia é que o viralflow possa ser utilizado em todas as etapas sem a permissão de root, especialmente na etapa de adição e atualização do catalogo do snpEff