diff --git a/.zenodo.json b/.zenodo.json index 4ee22bf7..28e072e8 100644 --- a/.zenodo.json +++ b/.zenodo.json @@ -2,7 +2,7 @@ "description": "

The pipeline

\n\n

bacannot, is a customisable, easy to use, pipeline that uses state-of-the-art software for comprehensively annotating prokaryotic genomes having only Docker and Nextflow as dependencies. It is able to annotate and detect virulence and resistance genes, plasmids, secondary metabolites, genomic islands, prophages, ICEs, KO, and more, while providing nice an beautiful interactive documents for results exploration.

", "license": "other-open", "title": "fmalmeida/bacannot: A generic but comprehensive bacterial annotation pipeline", - "version": "v3.1.1", + "version": "v3.1.2", "upload_type": "software", "creators": [ { diff --git a/docker/renv/build.sh b/docker/renv/build.sh index 51153a5c..a7bc2124 100644 --- a/docker/renv/build.sh +++ b/docker/renv/build.sh @@ -1 +1,2 @@ -../../bin/build_image.sh $1 +source ../set_version.sh +../../bin/build_image.sh $NEW_VERSION diff --git a/docker/renv/reports/report_custom_blast.Rmd b/docker/renv/reports/report_custom_blast.Rmd index 0a309f2a..9f19eb08 100644 --- a/docker/renv/reports/report_custom_blast.Rmd +++ b/docker/renv/reports/report_custom_blast.Rmd @@ -59,12 +59,10 @@ check_lines <- function(x) { ## Read input documents custom_blast <- try(read.delim(params$custom_blast, header = TRUE), silent = TRUE) -blast_gff <- try(read.delim(params$blast_gff, header = FALSE), silent = TRUE) -colnames(blast_gff) <- - c("Contig", "Source", "Feature", "Start", "End", "Score", "Strand", "Phase", "Attributes") +blast_gff <- try(read.delim(params$blast_gff, header = FALSE, col.names=c("Contig", "Source", "Feature", "Start", "End", "Score", "Strand", "Phase", "Attributes")), silent = TRUE) ## Check for emptyness -if (class(custom_blast) == "try-error" || +if (class(blast_gff) == "try-error" || check_lines(custom_blast) == 1) { custom_blast <- data.frame( matrix(ncol = 14, nrow = 0) @@ -72,6 +70,8 @@ if (class(custom_blast) == "try-error" || blast_gff <- data.frame( matrix(ncol = 9, nrow = 0) ) + colnames(blast_gff) <- + c("Contig", "Source", "Feature", "Start", "End", "Score", "Strand", "Phase", "Attributes") } else { # read blast summary @@ -91,6 +91,9 @@ if (class(custom_blast) == "try-error" || blast_gff$`Query Protein ID` <- getAttributeField(blast_gff$Attributes, "ID", ";") blast_gff$`Prokka Annotation (Gene)` <- getAttributeField(blast_gff$Attributes, "gene", ";") blast_gff$`Prokka Annotation (Product)` <- getAttributeField(blast_gff$Attributes, "product", ";") + + blast_gff <- blast_gff %>% + select(`Query Protein ID`, `Prokka Annotation (Gene)`, `Prokka Annotation (Product)`, `Custom DB Acc`, `Custom DB Target`, `Custom DB Product`, Attributes) } ``` @@ -144,10 +147,7 @@ Using the software bedtools intersect, the BLAST results have been used to searc
(#tab:blast-gff-table) Annotation intersection of the `r params$blast_db` custom database BLAST results with the main pipeline results ```{r} -blast <- blast_gff -# Render dt -datatable(blast %>% - select(`Query Protein ID`, `Prokka Annotation (Gene)`, `Prokka Annotation (Product)`, `Custom DB Acc`, `Custom DB Target`, `Custom DB Product`, Attributes), +datatable(blast_gff, escape = FALSE, filter = 'top', options = list(pageLength = 5, diff --git a/docs/images/nf-core-bacannot-compare_logo_dark.png b/docs/images/nf-core-bacannot-compare_logo_dark.png new file mode 100644 index 00000000..e69de29b diff --git a/lib/WorkflowMain.groovy b/lib/WorkflowMain.groovy index b966f0ee..7531147f 100755 --- a/lib/WorkflowMain.groovy +++ b/lib/WorkflowMain.groovy @@ -66,7 +66,7 @@ class WorkflowMain { // Download template samplesheet if (params.get_samplesheet) { - new File("bacannot_samplesheet.yaml").write(new URL ("https://github.com/fmalmeida/bacannot/raw/master/example_samplesheet.yml").getText()) + new File("bacannot_samplesheet.yaml").write(new URL ("https://github.com/fmalmeida/bacannot/raw/master/example_samplesheet.yaml").getText()) log.info """ Samplesheet (bacannot_samplesheet.yml) file saved in working directory Nice code! diff --git a/main.nf b/main.nf index fe88a9e3..f86a7eb3 100644 --- a/main.nf +++ b/main.nf @@ -52,11 +52,11 @@ workflow { Cheers. """) } else { - bacannot_db = file(params.bacannot_db) + bacannot_db = file(params.bacannot_db, checkIfExists: true) } // Load yaml - samplesheet_yaml = file(params.input) + samplesheet_yaml = file(params.input, checkIfExists: true) parameter_yaml = samplesheet_yaml.readLines().join("\n") new Yaml().load(parameter_yaml).each { k, v -> params[k] = v } diff --git a/markdown/CHANGELOG.md b/markdown/CHANGELOG.md index a4e8cb89..ffb67216 100644 --- a/markdown/CHANGELOG.md +++ b/markdown/CHANGELOG.md @@ -2,6 +2,18 @@ The tracking for changes started in v2.1 +## v3.1.2 + +This version contains: + +* A fix on the custom blast report file which had an wrong ifelse statement definition +* Updated version of renv docker with fixed report Rmd +* Addition of `checkIfExists` statements when loading file to make sure that user is pointing to files that exists and did not misspelled them +* Fixed a small misspelling on example samplesheet url +* A small fix on phigaro.nf module which was causing the pipeline to fail when its outputs were empty + +Thanks to @fetyj for spotting these issues. + ## v3.1.1 This version contains a quick fix spotted by @fetyj described in issue [#52](https://github.com/fmalmeida/bacannot/issues/52). Now the path to the argminer backup database is given as full path. diff --git a/modules/generic/custom_database_report.nf b/modules/generic/custom_database_report.nf index eb1d2d0c..2946466a 100644 --- a/modules/generic/custom_database_report.nf +++ b/modules/generic/custom_database_report.nf @@ -23,7 +23,7 @@ process CUSTOM_DATABASE_REPORT { system("rm -f input.??") ; system("rm -f input.?") ; - ## Generate Resistance Report + ## Generate Report rmarkdown::render("report_custom_blast.Rmd", params = list(\ blast_id = ${params.blast_custom_minid} , \ blast_cov = ${params.blast_custom_mincov}, \ diff --git a/modules/prophages/phigaro.nf b/modules/prophages/phigaro.nf index 318bc9d9..71a58d94 100644 --- a/modules/prophages/phigaro.nf +++ b/modules/prophages/phigaro.nf @@ -1,7 +1,6 @@ process PHIGARO { publishDir "${params.output}/${prefix}", mode: 'copy', saveAs: { filename -> - if (filename == "out.phg") null - else if (filename.indexOf("_version.txt") > 0) "tools_versioning/$filename" + if (filename.indexOf("_version.txt") > 0) "tools_versioning/$filename" else "prophages/phigaro/$filename" } tag "${prefix}" @@ -46,11 +45,12 @@ process PHIGARO { --not-open ; # change names - [ ! -s out.phg/assembly.phigaro.tsv ] || mv out.phg/assembly.phigaro.tsv ${prefix}_phigaro.tsv ; - [ ! -s out.phg/assembly.phigaro.html ] || mv out.phg/assembly.phigaro.html ${prefix}_phigaro.html ; + [ ! -s out.phg/assembly.phigaro.tsv ] || cp out.phg/assembly.phigaro.tsv ${prefix}_phigaro.tsv ; + [ ! -s out.phg/assembly.phigaro.html ] || cp out.phg/assembly.phigaro.html ${prefix}_phigaro.html ; # create BED - grep -v "taxonomy" ${prefix}_phigaro.tsv | \ - awk 'BEGIN { FS = "\t"; OFS="\\t" } { print \$1,\$2,\$3 }' > ${prefix}_phigaro.bed + touch ${prefix}_phigaro.bed ; + [ ! -s out.phg/assembly.phigaro.html ] || grep -v "taxonomy" ${prefix}_phigaro.tsv | \\ + awk 'BEGIN { FS = "\\t"; OFS="\\t" } { print \$1,\$2,\$3 }' > ${prefix}_phigaro.bed """ } diff --git a/nextflow.config b/nextflow.config index 80da7098..b86ba429 100644 --- a/nextflow.config +++ b/nextflow.config @@ -104,7 +104,7 @@ manifest { homePage = "https://github.com/fmalmeida/bacannot" mainScript = "main.nf" nextflowVersion = ">=20.10.0" - version = '3.1.1' + version = '3.1.2' } // Function to ensure that resource requirements don't go beyond diff --git a/workflows/parse_samples.nf b/workflows/parse_samples.nf index ed861ee8..6ee0c736 100644 --- a/workflows/parse_samples.nf +++ b/workflows/parse_samples.nf @@ -13,13 +13,13 @@ workflow PARSE_SAMPLESHEET { tuple( row.name, row.entrypoint, - (row.fwd == "missing_pairFWD") ? row.fwd : file(row.fwd), - (row.rev == "missing_pairREV") ? row.rev : file(row.rev), - (row.single == "missing_single") ? row.single : file(row.single), - (row.lreads == "missing_lreads") ? row.lreads : file(row.lreads), + (row.fwd == "missing_pairFWD") ? row.fwd : file(row.fwd, checkIfExists: true), + (row.rev == "missing_pairREV") ? row.rev : file(row.rev, checkIfExists: true), + (row.single == "missing_single") ? row.single : file(row.single, checkIfExists: true), + (row.lreads == "missing_lreads") ? row.lreads : file(row.lreads, checkIfExists: true), row.lr_type, - (row.fast5 == "missing_fast5") ? row.fast5 : file(row.fast5), - (row.assembly == "missing_assembly") ? row.assembly : file(row.assembly), + (row.fast5 == "missing_fast5") ? row.fast5 : file(row.fast5, checkIfExists: true), + (row.assembly == "missing_assembly") ? row.assembly : file(row.assembly, checkIfExists: true), row.resfinder ) }