From 7ea0980fc45b83f3dc0770edf1f8233ae933421a Mon Sep 17 00:00:00 2001 From: Jacques Dainat Date: Mon, 4 May 2026 16:22:19 +0200 Subject: [PATCH 1/5] Fix #46 Bug 1 --- config/multiqc_conf.yml | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/config/multiqc_conf.yml b/config/multiqc_conf.yml index 8484232..d3ebe23 100644 --- a/config/multiqc_conf.yml +++ b/config/multiqc_conf.yml @@ -1,5 +1,9 @@ title: "AliNe - Nextflow Alignment pipeline (https://github.com/Juke34/AliNe)" +# Raised from MultiQC default 50 MB: long-read (ONT/PacBio) samtools stats files +# routinely exceed 50 MB due to per-cycle tables spanning the full read length. Set to 200 MB. +log_filesize_limit: 200000000 + run_modules: - fastqc - fastp From f7bb4a9a551e721b77c6665d2cf56fff08e3d4ba Mon Sep 17 00:00:00 2001 From: Jacques Dainat Date: Mon, 4 May 2026 16:22:47 +0200 Subject: [PATCH 2/5] increment version --- nextflow.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow.config b/nextflow.config index 455b97e..7a6ff17 100644 --- a/nextflow.config +++ b/nextflow.config @@ -5,7 +5,7 @@ manifest { description = 'Nextflow alignment pipeline' mainScript = 'aline.nf' nextflowVersion = '>=22.04.0' - version = '1.6.3' + version = '1.6.4' } From 79fbf89dc5ec96d6f0585a7cfaac8337c865c28d Mon Sep 17 00:00:00 2001 From: Jacques Dainat Date: Tue, 5 May 2026 11:21:58 +0200 Subject: [PATCH 3/5] Fix #46 Bug 2 add extra info to run statistics at the end of the pipeline. Change final message --- aline.nf | 48 +++++++++++++++++++++++++++++++++++------------- 1 file changed, 35 insertions(+), 13 deletions(-) diff --git a/aline.nf b/aline.nf index 9fdecaa..7ea9716 100644 --- a/aline.nf +++ b/aline.nf @@ -1522,7 +1522,7 @@ def helpMSG() { fastqc output and supported aligner output. Usage example: - nextflow run aline.nf --reads /path/to/reads_{1,2}.fastq.gz --reference /path/to/reference.fa --outdir alignment_results --aligner bbmap,bowtie2 --fastqc true + nextflow run aline.nf --reads /path/to/reads_{1,2}.fastq.gz --reference /path/to/reference.fa --outdir alignment_results --aligner bbmap,bowtie2 --fastqc --samtools_stats --help prints the help section @@ -1717,26 +1717,48 @@ workflow.onComplete { // Log colors ANSI codes c_reset = params.monochrome_logs ? '' : "\033[0m"; + c_dim = params.monochrome_logs ? '' : "\033[2m"; + c_black = params.monochrome_logs ? '' : "\033[0;30m"; c_green = params.monochrome_logs ? '' : "\033[0;32m"; + c_yellow = params.monochrome_logs ? '' : "\033[0;33m"; + c_blue = params.monochrome_logs ? '' : "\033[0;34m"; + c_purple = params.monochrome_logs ? '' : "\033[0;35m"; + c_cyan = params.monochrome_logs ? '' : "\033[0;36m"; + c_white = params.monochrome_logs ? '' : "\033[0;37m"; c_red = params.monochrome_logs ? '' : "\033[0;31m"; - if (workflow.success) { - log.info "\n${c_green} AliNe pipeline complete!${c_reset}" - } else { - log.error "${c_red}Oops .. something went wrong${c_reset}" - } + def status_icon = workflow.success ? "${c_green}[OK]${c_reset}" : "${c_red}[FAILED]${c_reset}" + def error_line = workflow.errorReport ? "\n ${c_red} Error : ${workflow.errorReport}${c_reset}" : '' - log.info " The results are available in the ‘${params.outdir}’ directory." log.info """ - AliNe Pipeline execution summary - -------------------------------------- - Completed at : ${workflow.complete} - UUID : ${workflow.sessionId} + ${c_cyan}+----------------------------------------------------+ + | AliNe Pipeline v${workflow.manifest.version} -- Run Summary | + +----------------------------------------------------+${c_reset} + Status : ${status_icon} + Completed at : ${workflow.complete.format('dd-MMM-yyyy HH:mm:ss')} Duration : ${workflow.duration} - Success : ${workflow.success} - Exit Status : ${workflow.exitStatus} + CPU hours : ${workflow.stats.computeTimeFmt} + Succeeded : ${workflow.stats.succeedCount} + Cached : ${workflow.stats.cachedCount} + Session ID : ${c_dim}${workflow.sessionId}${c_reset} + Exit status : ${workflow.exitStatus}${error_line} Error report : ${workflow.errorReport ?: '-'} + + The results are available in the ${c_blue}alignment_results_illumina_paired${c_reset} directory. """ + + if (workflow.success) { + def tips = [] + if (!params.fastqc && !params.samtools_stats) { + tips << "${c_yellow} Tip: use --fastqc and/or --samtools_stats to get statistics.${c_reset}" + } else if (!params.fastqc) { + tips << "${c_yellow} Tip: use --fastqc to get additional QC statistics on raw and aligned reads.${c_reset}" + } else if (!params.samtools_stats) { + tips << "${c_yellow} Tip: use --samtools_stats to get additional alignment statistics.${c_reset}" + } + if (tips) log.info tips.join('\n') + } + log.info ('\n') } /* From da91541f12bed6bd5640ac90bc7f31e69d2c2c2a Mon Sep 17 00:00:00 2001 From: Jacques Dainat Date: Tue, 5 May 2026 11:22:21 +0200 Subject: [PATCH 4/5] change comment --- aline.nf | 4 ---- 1 file changed, 4 deletions(-) diff --git a/aline.nf b/aline.nf index 7ea9716..cb7923b 100644 --- a/aline.nf +++ b/aline.nf @@ -1762,10 +1762,6 @@ workflow.onComplete { } /* -Other aligner? - - to map ont? - - dragmap - How to add an aliger ? ----------------------- Add a module, From 6ce848de83dde86b4fd1cb62fbc8201d06fc53ae Mon Sep 17 00:00:00 2001 From: Jacques Dainat Date: Tue, 5 May 2026 11:37:50 +0200 Subject: [PATCH 5/5] add end message to report issue, star the repo, etc --- aline.nf | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/aline.nf b/aline.nf index cb7923b..1b01c64 100644 --- a/aline.nf +++ b/aline.nf @@ -1758,7 +1758,14 @@ workflow.onComplete { } if (tips) log.info tips.join('\n') } - log.info ('\n') + log.info """ + ${c_dim}-------------------------------------------------- + Enjoying AliNe? You can help by: + • Starring the repo : https://github.com/Juke34/AliNe + • Reporting issues : https://github.com/Juke34/AliNe/issues + • Joining discussions: https://github.com/Juke34/AliNe/discussions + --------------------------------------------------${c_reset} + """ } /*