release of ViralFlow version 1.0.0 #40
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* [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]>
cleaning unnecessary lines Co-authored-by: dezordi <[email protected]>
cleaning unnecessary line Co-authored-by: dezordi <[email protected]>
fix compileOutput.py script to run on viralflow env
Develop fix nextflow metrics
fix splitting of R1 and R2 unmapped reads
Fix intrahost script to run on viralflow env
Implementation of coveragePlot module
solving fixWGS to run on viralflow env
…e instead sandbox. PS: snpeff, pangolin and nextclade still in sandbox
Develop update containers
alexandrefreitasdasilva
requested review from
dezordi,
AMarinhoSN and
costahud
dezordi
approved these changes
Nov 20, 2023
costahud
approved these changes
Nov 20, 2023
This was referenced Nov 20, 2023
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This PR implements all planned improvements and new features to release ViralFlow 1.0.0.
Closes #23
Closes #17
Closes #16
Closes #15