-[](https://doi.org/10.5281/zenodo.3627669)
+[](https://doi.org/10.12688/f1000research.139488.1)
[](https://github.com/fmalmeida/bacannot/releases)
[](https://bacannot.readthedocs.io/en/latest/?badge=latest)
[](https://www.nextflow.io/)
@@ -8,6 +8,7 @@
[](https://sylabs.io/docs/)
[](https://github.com/fmalmeida/bacannot/blob/master/LICENSE)
[](https://twitter.com/fmarquesalmeida)
+[](https://doi.org/10.5281/zenodo.3627669)
[](https://gitpod.io/github.com/fmalmeida/bacannot)
@@ -87,16 +88,7 @@ These images have been kept separate to not create massive Docker image and to a
## Installation
-1. If you don't have it already install [Docker](https://docs.docker.com/) in your computer.
- * After installed, you need to download the required Docker images
-
- ```bash
- docker pull fmalmeida/bacannot:v3.3_misc ;
- docker pull fmalmeida/bacannot:v3.3_renv ;
- docker pull fmalmeida/bacannot:jbrowse ;
- ```
-
-๐ฅ Nextflow can also automatically handle images download on the fly when executed. All the other docker images from **biocontainers** are downloaded automatically. If docker has exceeded its download limit rates, please try again in a few hours.
+1. If you don't have it already install either [Docker](https://docs.docker.com/) or [Singularity](https://docs.sylabs.io/guides/3.5/user-guide/index.html) in your computer.
2. Install Nextflow (version 20.10 or higher):
@@ -110,54 +102,7 @@ These images have been kept separate to not create massive Docker image and to a
๐ฅ Users can get let the pipeline always updated with: `nextflow pull fmalmeida/bacannot`
-### Downloading and updating databases
-
-Bacannot databases are not inside the docker images anymore to avoid huge images and problems with connections and limit rates with dockerhub.
-
-#### Pre-formatted
-
-Users can directly download pre-formatted databases from Zenodo: https://doi.org/10.5281/zenodo.7615811
-
-Useful for standardization and also overcoming known issues that may arise when formatting databases with `singularity` profile.
-
-A module to download the latest pre-formatted database has also been made available:
-```bash
-# Download pipeline pre-built databases
-nextflow run fmalmeida/bacannot --get_zenodo_db --output ./ -profile 
-[](https://doi.org/10.5281/zenodo.3627669)
+[](https://doi.org/10.12688/f1000research.139488.1)
[](https://github.com/fmalmeida/bacannot/releases)
[](https://bacannot.readthedocs.io/en/latest/?badge=latest)
[](https://www.nextflow.io/)
@@ -10,6 +10,7 @@
[](https://sylabs.io/docs/)
[](https://github.com/fmalmeida/bacannot/blob/master/LICENSE)
[](https://twitter.com/fmarquesalmeida)
+[](https://doi.org/10.5281/zenodo.3627669)
## About
diff --git a/docs/installation.md b/docs/installation.md
index 5056467d..2bc4a5fa 100644
--- a/docs/installation.md
+++ b/docs/installation.md
@@ -19,17 +19,30 @@ nextflow pull fmalmeida/bacannot
## Downloading docker images
-The custom docker images used by the pipeline are:
+> The pipeline uses both custom and public images.
+> All images can be downloaded on the fly, automatically by nextflow, and this is the recommended way to do it.
+
+If you want to download it yourself, you can find all the images used in the pipeline described in the file [docker.config](https://github.com/fmalmeida/bacannot/blob/master/conf/docker.config) (for docker) and [singularity.config](https://github.com/fmalmeida/bacannot/blob/master/conf/singularity.config) (for singularity).
+
+The images are defined like the following:
```bash
-docker pull fmalmeida/bacannot:v3.3_misc ;
-docker pull fmalmeida/bacannot:v3.3_renv ;
-docker pull fmalmeida/bacannot:jbrowse ;
+...
+withLabel: 'db_download|db_tools|misc' {
+ container = 'fmalmeida/bacannot@sha256:bdb31637cacf99736656ab3b69f1f01ba1b5eb026771d5c266b4c84e96153057'
+}
+...
```
-> The pipeline also uses other public images available in biocontainers. All images can be downloaded on the fly, automatically be nextflow.
+And could be downloaded like this:
+
+```bash
+docker pull fmalmeida/bacannot@sha256:bdb31637cacf99736656ab3b69f1f01ba1b5eb026771d5c266b4c84e96153057
+```
-!!! info "Using singularity"
+> You would need to do it for each image.
+
+!!! info "If using singularity"
**Docker and singularity images are downloaded on the fly**. Be sure to properly set `NXF_SINGULARITY_LIBRARYDIR` env variable to a writable directory if using Singularity. This will make that the downloaded images are reusable through different executions. Read more at: https://www.nextflow.io/docs/latest/singularity.html#singularity-docker-hub
@@ -39,17 +52,56 @@ docker pull fmalmeida/bacannot:jbrowse ;
# apply this command to each image
# just change the "/" and ":" for "-".
# E.g. Image fmalmeida/bacannot:v3.3_misc becomes fmalmeida-bacannot-v3.3_misc.img
- singularity pull --dir $NXF_SINGULARITY_LIBRARYDIR fmalmeida-bacannot-v3.3_misc.img docker://fmalmeida/bacannot:v3.3_misc
+ # for singularity --> prepare env variables
+ # remember to properly set NXF_SINGULARITY_LIBRARYDIR
+ # read more at https://www.nextflow.io/docs/latest/singularity.html#singularity-docker-hub
+ export NXF_SINGULARITY_LIBRARYDIR=Parameter
| Required | Default | Description |
+| Parameter
| Required | Default | Description |
| :--------------------------------------- | :------- | :------ | :---------- |
| `--input` | :material-check: | NA | Input samplesheet describing all the samples to be analysed |
+| `--enable_deduplication` | :material-close: | false | Run deduplication command on input reads before assembly. Only useful for samples where reads are given instead of a genome fasta. |
| `--output` | :material-check: | results | Name of directory to store output values. A sub-directory for each genome will be created inside this main directory. |
| `--bacannot_db` | :material-check: | NA | Path for root directory containing required bacannot databases |
@@ -45,6 +46,7 @@ The pipeline accepts as input two other input files types that are used to perfo
| :--------------------------------------- | :------- | :------ | :---------- |
| `--get_dbs` | :material-close: | false | Instead of running the analysis workflow, it will try to download required databases and save them in `--output` |
| `--force_update` | :material-close: | false | Instead of only downloading missing databases, download everything again and overwrite. |
+| `--get_zenodo_db` | :material-close: | false | Download pre-built databases stored in zenodo. [See quickstart](quickstart.md#).
!!! tip ""
@@ -94,6 +96,8 @@ The use of this parameter sets a default value for input samples. If a sample ha
| `--skip_prophage_search` | :material-close: | false | Tells whether not to run prophage annotation modules |
| `--skip_kofamscan` | :material-close: | false | Tells whether not to run KEGG orthology (KO) annotation with KofamScan |
| `--skip_antismash` | :material-close: | false | Tells whether or not to run antiSMASH (secondary metabolite) annotation. AntiSMASH is executed using only its core annotation modules in order to keep it fast. |
+| `--skip_circos` | :material-close: | false | Tells whether or not to run the final `CIRCOS` module. When the input genome has many contigs, its results are not meaningful. |
+| `--skip_integron_finder` | :material-close: | false | Tells whether or not to run the integron finder tool. |
## Custom databases
diff --git a/docs/quickstart.md b/docs/quickstart.md
index 5490726f..42b5ee89 100644
--- a/docs/quickstart.md
+++ b/docs/quickstart.md
@@ -102,4 +102,4 @@ nextflow run fmalmeida/bacannot -profile docker,quicktest --bacannot_db ./bacann
### Annotation with bakta
-User can also perform the core generic annotation with bakta instead of prokka. Please read [the manual](manual#bakta-annotation).
+User can also perform the core generic annotation with bakta instead of prokka. Please read [the manual](manual.md#bakta-annotation).
diff --git a/docs/requirements.txt b/docs/requirements.txt
index d5ff7eda..42c51dbf 100644
--- a/docs/requirements.txt
+++ b/docs/requirements.txt
@@ -14,4 +14,5 @@ mergedeep>=1.3.4
colorama>=0.4; platform_system == 'Windows'
mkdocs-pymdownx-material-extras
mkdocs-git-revision-date-plugin
-mkdocs-material
\ No newline at end of file
+mkdocs-material
+mkdocs-macros-plugin
\ No newline at end of file
diff --git a/lib/WorkflowMain.groovy b/lib/WorkflowMain.groovy
index 57d85384..6ccb1c75 100755
--- a/lib/WorkflowMain.groovy
+++ b/lib/WorkflowMain.groovy
@@ -10,7 +10,7 @@ class WorkflowMain {
public static String citation(workflow) {
return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" +
"* The pipeline\n" +
- " https://doi.org/10.5281/zenodo.3627669\n\n" +
+ " https://doi.org/10.12688/f1000research.139488.1\n\n" +
"* The nf-core framework\n" +
" https://doi.org/10.1038/s41587-020-0439-x\n\n" +
"* Software dependencies\n" +
diff --git a/markdown/CHANGELOG.md b/markdown/CHANGELOG.md
index fcd33376..03654f50 100644
--- a/markdown/CHANGELOG.md
+++ b/markdown/CHANGELOG.md
@@ -2,12 +2,35 @@
The tracking for changes started in v2.1
-## v3.3 [TBD]
+## v3.3.3 [11-March-2024]
+
+* [[#118](https://github.com/fmalmeida/bacannot/issues/116)]
+ * Add a parameter to allow user to skip `INTEGRON_FINDER` execution.
+ * Add a parameter to allow user to skip `CIRCOS` execution.
+* Split antismash docker image, and added some snippets to fix some workarounds to allow pipeline to run with singularity
+
+## v3.3.2 [09-February-2024]
+
+* [[#116](https://github.com/fmalmeida/bacannot/issues/116)] -- Small update to avoid having `integron_finder` gbks with start position as 0, since it breaks conversion to gff.
+
+## v3.3.1 [29-October-2023]
+
+* [[#111](https://github.com/fmalmeida/bacannot/issues/111)] -- Updated `falmeida-py` package version to fix problem with missing key for Summary.
+
+## v3.3 [01-October-2023]
* [[#50](https://github.com/fmalmeida/bacannot/issues/50)] -- Add `Integron Finder` tool to the pipeline
-* [#69](https://github.com/fmalmeida/bacannot/issues/69) -- Change how tools use docker images in order to:
+* [[#69](https://github.com/fmalmeida/bacannot/issues/69)] -- Change how tools use docker images in order to:
* make tools use public bioconda images whenever possible to allow easy addition of tools and avoid much conflicts in docker images
* dimish the size and tools inside the docker images, the docker images now are only built to contain tools and all required for modules that cannot just use bioconda docker images.
+* [[#81](https://github.com/fmalmeida/bacannot/issues/81)] -- Add `MOB Suite` tool to the pipeline
+* [[#85](https://github.com/fmalmeida/bacannot/issues/85)] -- Include checkup on header size for Prokka
+* [[#98](https://github.com/fmalmeida/bacannot/issues/98)] -- Add ICEberg and PHAST blastp results to json summary
+* [[#100](https://github.com/fmalmeida/bacannot/issues/100)] -- Update pipeline to use docker shasum instead of tags
+* [[#107](https://github.com/fmalmeida/bacannot/issues/107)] -- Add a parameter, `--enable_deduplication` for deduplicating input reads before assembly
+* Update unicycler docker image to latest '0.5.0--py310h6cc9453_3' to avoid errors originated from previous image containing buggy installation.
+* Other minor changes / updates highlited in [[#93](https://github.com/fmalmeida/bacannot/pull/93)]
+
## v3.2 [19-December-2022]
* Fixes https://github.com/fmalmeida/bacannot/issues/68 reported by @lam-c
diff --git a/mkdocs.yml b/mkdocs.yml
index 58482435..1a5157ba 100644
--- a/mkdocs.yml
+++ b/mkdocs.yml
@@ -22,6 +22,8 @@ theme:
repo: fontawesome/brands/github-alt
plugins:
- git-revision-date
+ - search
+ - macros
markdown_extensions:
- pymdownx.emoji:
emoji_index: !!python/name:materialx.emoji.twemoji
diff --git a/modules/MGEs/digIS.nf b/modules/MGEs/digIS.nf
index 665abf60..a1ad29aa 100644
--- a/modules/MGEs/digIS.nf
+++ b/modules/MGEs/digIS.nf
@@ -18,14 +18,8 @@ process DIGIS {
script:
"""
- # activate env
- source activate digIS
-
# run digIS
- python3 \$(which digIS_search.py) -i $genome -g $genbank -o digIS
-
- # deactivate env
- conda deactivate
+ conda run -n digIS python3 \$(which digIS_search.py) -i $genome -g $genbank -o digIS
# parse digIS to get nucleotide and aminoacide
# also put ids in uppercase
diff --git a/modules/MGEs/integron_finder.nf b/modules/MGEs/integron_finder.nf
index b06fccdf..1cbfc14e 100644
--- a/modules/MGEs/integron_finder.nf
+++ b/modules/MGEs/integron_finder.nf
@@ -1,7 +1,7 @@
process INTEGRON_FINDER {
- publishDir "${params.output}", mode: 'copy', saveAs: { filename ->
+ publishDir "${params.output}/${prefix}", mode: 'copy', saveAs: { filename ->
if (filename.indexOf("_version.txt") > 0) "tools_versioning/$filename"
- else "${prefix}/integron_finder/$filename"
+ else "integron_finder/$filename"
}
tag "${prefix}"
label = [ 'process_medium' ]
diff --git a/modules/MGEs/integron_finder_2gff.nf b/modules/MGEs/integron_finder_2gff.nf
index 6abaeab3..f314c748 100644
--- a/modules/MGEs/integron_finder_2gff.nf
+++ b/modules/MGEs/integron_finder_2gff.nf
@@ -12,13 +12,13 @@ process INTEGRON_FINDER_2GFF {
script:
def args = task.ext.args ?: ''
"""
+ # fix 0-based sequences
+ sed -e 's/ 0\\.\\./ 1\\.\\./g' -e 's/complement(0\\.\\./complement(1\\.\\./g' $gbk > fixed.gbk
+
# convert to gff if available
- touch ${prefix}_integrons.gff ;
- for gbk in \$(ls *.gbk) ; do
- conda run -n perl bp_genbank2gff3 \$gbk -o - | \
- grep 'integron_id' | \
- sed 's|ID=.*integron_id=|ID=|g' | \
- sed 's/GenBank/Integron_Finder/g' >> ${prefix}_integrons.gff
- done
+ conda run -n perl bp_genbank2gff3 fixed.gbk -o - | \\
+ grep 'integron_id' | \\
+ sed 's|ID=.*integron_id=|ID=|g' | \\
+ sed 's/GenBank/Integron_Finder/g' >> ${prefix}_integrons.gff
"""
}
diff --git a/modules/MGEs/mob_suite.nf b/modules/MGEs/mob_suite.nf
index 14256e92..0ae1c3d3 100644
--- a/modules/MGEs/mob_suite.nf
+++ b/modules/MGEs/mob_suite.nf
@@ -1,7 +1,7 @@
process MOBSUITE {
- publishDir "${params.output}", mode: 'copy', saveAs: { filename ->
+ publishDir "${params.output}/${prefix}", mode: 'copy', saveAs: { filename ->
if (filename.indexOf("_version.txt") > 0) "tools_versioning/$filename"
- else "${prefix}/plasmids/mob_suite/$filename"
+ else "plasmids/mob_suite/$filename"
}
tag "${prefix}"
label = [ 'process_medium' ]
diff --git a/modules/assembly/flye.nf b/modules/assembly/flye.nf
index 5bbc4668..d588d01e 100644
--- a/modules/assembly/flye.nf
+++ b/modules/assembly/flye.nf
@@ -18,14 +18,21 @@ process FLYE {
script:
lr = (lr_type == 'nanopore') ? '--nano-raw' : '--pacbio-raw'
+ dedup_lr = params.enable_deduplication ?
+ "gunzip -cf $lreads | awk '{if(NR%4==1) \$0=sprintf(\"@1_%d\",(1+i++)); print;}' | gzip -c > ${prefix}_deduplicated_reads.fastq.gz" :
+ "ln -s $lreads ${prefix}_deduplicated_reads.fastq.gz"
+
"""
# Save flye version
flye -v > flye_version.txt ;
+ # remove duplicate reads
+ $dedup_lr
+
# Run flye
flye \\
${lr} \\
- $lreads \\
+ ${prefix}_deduplicated_reads.fastq.gz \\
--out-dir flye_${prefix} \\
--threads $task.cpus &> flye.log ;
diff --git a/modules/assembly/unicycler.nf b/modules/assembly/unicycler.nf
index 032a3957..145f1c1f 100644
--- a/modules/assembly/unicycler.nf
+++ b/modules/assembly/unicycler.nf
@@ -17,14 +17,55 @@ process UNICYCLER {
path('unicycler_version.txt'), emit: version
script:
- unpaired_param = (sreads.getName() != "input.3") ? "-s $sreads" : ""
- paired_param = (sread1.getName() != "input.1" && sread2.getName() != "input.2") ? "-1 $sread1 -2 $sread2" : ""
- lr_param = (lreads.getName() != "input.4") ? "-l $lreads" : ""
+ unpaired_param = ""
+ dedup_sreads = ""
+ paired_param = ""
+ dedup_paired = ""
+ lr_param = ""
+ dedup_lr = ""
+
+ // sreads
+ if (sreads.getName() != "input.3") {
+
+ dedup_sreads = params.enable_deduplication ?
+ "gunzip -cf $sreads | awk '{if(NR%4==1) \$0=sprintf(\"@1_%d\",(1+i++)); print;}' | gzip -c > ${prefix}_deduplicated_sreads.fastq.gz" :
+ "ln -s $sreads ${prefix}_deduplicated_sreads.fastq.gz"
+
+ unpaired_param = "-s ${prefix}_deduplicated_sreads.fastq.gz"
+
+ }
+
+ // paired
+ if (sread1.getName() != "input.1" && sread2.getName() != "input.2") {
+
+ dedup_paired = params.enable_deduplication ?
+ "gunzip -cf $sread1 | awk '{if(NR%4==1) \$0=sprintf(\"@1_%d\",(1+i++)); print;}' | gzip -c > ${prefix}_deduplicated_sread_R1.fastq.gz && gunzip -cf $sread2 | awk '{if(NR%4==1) \$0=sprintf(\"@1_%d\",(1+i++)); print;}' | gzip -c > ${prefix}_deduplicated_sread_R2.fastq.gz" :
+ "ln -s $sread1 ${prefix}_deduplicated_sread_R1.fastq.gz && ln -s $sread2 ${prefix}_deduplicated_sread_R2.fastq.gz"
+
+ paired_param = "-1 ${prefix}_deduplicated_sread_R1.fastq.gz -2 ${prefix}_deduplicated_sread_R2.fastq.gz"
+
+ }
+
+ // lreads
+ if (lreads.getName() != "input.4") {
+
+ dedup_lr = params.enable_deduplication ?
+ "gunzip -cf $lreads | awk '{if(NR%4==1) \$0=sprintf(\"@1_%d\",(1+i++)); print;}' | gzip -c > ${prefix}_deduplicated_lreads.fastq.gz" :
+ "ln -s $lreads ${prefix}_deduplicated_lreads.fastq.gz"
+
+ lr_param = "-l $lreads"
+
+ }
"""
# Save unicycler version
unicycler --version > unicycler_version.txt
+ # remove duplicate reads
+ $dedup_sreads
+ $dedup_paired
+ $dedup_lr
+
# Run unicycler
unicycler \\
$paired_param \\
diff --git a/modules/bacannot_dbs/antismash.nf b/modules/bacannot_dbs/antismash.nf
index 5e9b8962..e554f9ff 100644
--- a/modules/bacannot_dbs/antismash.nf
+++ b/modules/bacannot_dbs/antismash.nf
@@ -6,9 +6,33 @@ process ANTISMASH_DB {
file("*")
script:
+ def antismash_version='6.1.1'
+
+ if (params.running_engine == 'singularity')
+ """
+ mkdir local-install
+ export PYTHONUSERBASE=./local-install
+ export PATH=/opt/conda/envs/antismash/bin:\$PATH
+
+ # install locally so it can download dbs
+ # singularity has many read-write permissions for this tool
+ wget https://dl.secondarymetabolites.org/releases/${antismash_version}/antismash-${antismash_version}.tar.gz
+ tar zxvf antismash-${antismash_version}.tar.gz
+ python -m pip install --user ./antismash-${antismash_version}
+ export PYTHONPATH=\$(realpath \$( find ./local-install -name 'site-packages' ))
+
+ # now download it
+ # download antismash database
+ ./local-install/bin/download-antismash-databases --database-dir ./
+
+ # delete it
+ rm -rf ./local-install ./antismash-${antismash_version}*
+ """
+
+ else
"""
# download antismash database
export PATH=/opt/conda/envs/antismash/bin:\$PATH
- download-antismash-databases --database-dir \$(pwd)
+ download-antismash-databases --database-dir ./
"""
}
diff --git a/modules/generic/antismash.nf b/modules/generic/antismash.nf
index 207c12d4..b56df0a5 100644
--- a/modules/generic/antismash.nf
+++ b/modules/generic/antismash.nf
@@ -6,6 +6,8 @@ process ANTISMASH {
tag "${prefix}"
label = [ 'misc', 'process_medium' ]
+ // if (params.running_engine = 'singularity') { runOptions = '--writable-tmpfs -e --no-home -B $PWD' }
+
input:
tuple val(prefix), file(genbank)
file(bacannot_db)
@@ -18,10 +20,69 @@ process ANTISMASH {
script:
def gbk_suffix = (params.bakta_db) ? "gbff" : "gbk"
def gbk_prefix = "${genbank.baseName}" - "${gbk_suffix}"
- """
- # Activate env
+ def antismash_version='6.1.1'
+
+ if (params.running_engine == 'singularity')
+ """
+ # Get tool version
+ antismash --version > antismash_version.txt ;
+
+ # activate env
+ mkdir local-install
+ export PYTHONUSERBASE=./local-install
export PATH=/opt/conda/envs/antismash/bin:\$PATH
+
+ # singularity has many read-write permissions for this tool
+ wget https://dl.secondarymetabolites.org/releases/${antismash_version}/antismash-${antismash_version}.tar.gz
+ tar zxvf antismash-${antismash_version}.tar.gz
+ python -m pip install --user ./antismash-${antismash_version}
+ export PYTHONPATH=\$(realpath \$( find ./local-install -name 'site-packages' ))
+
+ # Run tool
+ ./local-install/bin/antismash \\
+ --output-dir antiSMASH \\
+ --genefinding-tool none \\
+ --databases ${bacannot_db}/antismash_db \\
+ -c $task.cpus \\
+ $genbank ;
+
+ # enter results dir
+ cd antiSMASH ;
+
+ # produce gff from main results
+ seqret \\
+ -sequence ${gbk_prefix}.gbk \\
+ -feature \\
+ -fformat genbank \\
+ -fopenfile ${gbk_prefix}.gbk \\
+ -osformat gff \\
+ -osname_outseq ${gbk_prefix} \\
+ -auto ;
+
+ # get the locus tags annotated as list
+ # only when results exist
+ if ls *region*gbk 1> /dev/null 2>&1; then
+
+ grep \\
+ "locus_tag" \\
+ *region*gbk | \\
+ cut \\
+ -f 2 \\
+ -d "=" | \\
+ tr -d '"' | \\
+ sort -u > gene_ids.lst ;
+
+ # subset regions GFF from main GFF for JBrowse
+ grep \\
+ -w \\
+ -f gene_ids.lst \\
+ ${gbk_prefix}.gff > regions.gff ;
+ fi
+ """
+
+ else
+ """
# Get tool version
antismash --version > antismash_version.txt ;
@@ -29,10 +90,10 @@ process ANTISMASH {
antismash \\
--output-dir antiSMASH \\
--genefinding-tool none \\
- -c $task.cpus \\
--databases ${bacannot_db}/antismash_db \\
+ -c $task.cpus \\
$genbank ;
-
+
# enter results dir
cd antiSMASH ;
@@ -67,4 +128,5 @@ process ANTISMASH {
fi
"""
+
}
diff --git a/modules/resistance/resfinder.nf b/modules/resistance/resfinder.nf
index 9b7105e9..017efffa 100644
--- a/modules/resistance/resfinder.nf
+++ b/modules/resistance/resfinder.nf
@@ -24,6 +24,7 @@ process RESFINDER {
"""
# activate env
source activate resfinder
+ export PATH=/opt/conda/envs/resfinder/lib/python3.12/site-packages/resfinder/:\$PATH
# Run resfinder acquired resistance
run_resfinder.py \\
diff --git a/nextflow.config b/nextflow.config
index 1afb0454..b0654f31 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -13,7 +13,6 @@ includeConfig 'conf/defaults.config'
params {
// Boilerplate options
- tracedir = "${params.output}/pipeline_info"
plaintext_email = false
monochrome_logs = false
help = false
@@ -23,7 +22,7 @@ params {
get_samplesheet = false
validate_params = true
show_hidden_params = false
- schema_ignore_params = 'enable_conda,monochrome_logs,plaintext_email'
+ schema_ignore_params = 'enable_conda,monochrome_logs,plaintext_email,running_engine'
enable_conda = false
monochrome_logs = false
@@ -84,19 +83,19 @@ process.shell = ['/bin/bash', '-euo', 'pipefail']
def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
timeline {
enabled = true
- file = "${params.tracedir}/bacannot_timeline_${trace_timestamp}.html"
+ file = "${params.output}/pipeline_info/bacannot_timeline_${trace_timestamp}.html"
}
report {
enabled = true
- file = "${params.tracedir}/bacannot_report_${trace_timestamp}.html"
+ file = "${params.output}/pipeline_info/bacannot_report_${trace_timestamp}.html"
}
trace {
enabled = true
- file = "${params.tracedir}/bacannot_trace_${trace_timestamp}.txt"
+ file = "${params.output}/pipeline_info/bacannot_trace_${trace_timestamp}.txt"
}
dag {
enabled = true
- file = "${params.tracedir}/bacannot_pipeline_dag_${trace_timestamp}.svg"
+ file = "${params.output}/pipeline_info/bacannot_pipeline_dag_${trace_timestamp}.svg"
}
/*
@@ -109,7 +108,7 @@ manifest {
homePage = "https://github.com/fmalmeida/bacannot"
mainScript = "main.nf"
nextflowVersion = "!>=22.10.1"
- version = '3.3'
+ version = '3.3.3'
}
// Function to ensure that resource requirements don't go beyond
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 287901ca..416ad42b 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -34,6 +34,10 @@
"type": "string",
"description": "Path to input samplesheet"
},
+ "enable_deduplication": {
+ "type": "boolean",
+ "description": "Execute deduplication on reads before assembly."
+ },
"output": {
"type": "string",
"description": "Path for output directory",
@@ -59,15 +63,18 @@
"properties": {
"max_cpus": {
"type": "integer",
- "default": 16
+ "default": 16,
+ "description": "Maximum number of cpus a single module can use."
},
"max_memory": {
"type": "string",
- "default": "20.GB"
+ "default": "20.GB",
+ "description": "Maximum memory a single module can use."
},
"max_time": {
"type": "string",
- "default": "40.h"
+ "default": "40.h",
+ "description": "Maximum time a module can run."
}
}
},
@@ -146,6 +153,12 @@
"help_text": "If true, the process will be skipped!",
"hidden": true
},
+ "skip_circos": {
+ "type": "boolean",
+ "description": "Skip (do not run) circos?",
+ "help_text": "If true, the process will be skipped!",
+ "hidden": true
+ },
"skip_plasmid_search": {
"type": "boolean",
"description": "Skip (do not run) plasmidfinder?",
@@ -170,6 +183,12 @@
"help_text": "If true, the process will be skipped!",
"hidden": true
},
+ "skip_integron_finder": {
+ "type": "boolean",
+ "description": "Skip (do not run) integron finder?",
+ "help_text": "If true, the process will be skipped!",
+ "hidden": true
+ },
"skip_prophage_search": {
"type": "boolean",
"description": "Skip (do not run) prophage annotation?",
@@ -181,6 +200,12 @@
"description": "Skip (do not run) KO annotation?",
"help_text": "If true, the process will be skipped!",
"hidden": true
+ },
+ "skip_sourmash": {
+ "type": "boolean",
+ "description": "Skip (do not run) sourmash tool?",
+ "help_text": "If true, the process will be skipped!",
+ "hidden": true
}
},
"fa_icon": "fas fa-tasks"
@@ -339,13 +364,6 @@
"help_text": "Number of minimum overlapping base pairs required for merging\nNegative values, such as -20, means the number of required overlapping bases for merging.\nPositive values, such as 5, means the maximum distance accepted between features for merging.\nBy default (if Blank), this process is not executed. For execution the user needs to provide a value",
"description": "Minimum overlapping base pairs required for merging"
},
- "tracedir": {
- "type": "string",
- "description": "Directory to keep pipeline Nextflow logs and reports.",
- "default": "results/pipeline_info",
- "fa_icon": "fas fa-cogs",
- "hidden": true
- },
"validate_params": {
"type": "boolean",
"description": "Boolean whether to validate parameters against the schema at runtime",
@@ -363,9 +381,7 @@
"unicycler_version": {
"type": "string",
"description": "Select quay.io image tag for tool",
- "default": "0.4.8--py38h8162308_3",
- "hidden": true,
- "help_text": "Select a different version of tool based on the bioconda containers tag."
+ "default": "0.5.0--py310h6cc9453_3"
},
"flye_version": {
"type": "string",
diff --git a/workflows/bacannot.nf b/workflows/bacannot.nf
index ffeac379..039bc6c9 100644
--- a/workflows/bacannot.nf
+++ b/workflows/bacannot.nf
@@ -143,8 +143,13 @@ workflow BACANNOT {
ISLANDPATH( annotation_out_ch.gbk )
// Integron_finder software
- INTEGRON_FINDER( annotation_out_ch.genome )
- INTEGRON_FINDER_2GFF( INTEGRON_FINDER.out.gbk )
+ if (!params.skip_integron_finder) {
+ INTEGRON_FINDER( annotation_out_ch.genome )
+ INTEGRON_FINDER_2GFF( INTEGRON_FINDER.out.gbk )
+ ch_integron_finder_gff = INTEGRON_FINDER_2GFF.out.gff
+ } else {
+ ch_integron_finder_gff = Channel.empty()
+ }
// Virulence search
if (params.skip_virulence_search == false) {
@@ -327,7 +332,7 @@ workflow BACANNOT {
.join(phast_output_ch, remainder: true)
.join(DIGIS.out.gff, remainder: true)
.join(ch_custom_annotations, remainder: true)
- .join(INTEGRON_FINDER_2GFF.out.gff, remainder: true)
+ .join(ch_integron_finder_gff, remainder: true)
)
/*
@@ -367,7 +372,7 @@ workflow BACANNOT {
.join( MERGE_ANNOTATIONS.out.digis_gff )
.join( antismash_output_ch, remainder: true )
.join( MERGE_ANNOTATIONS.out.customdb_gff.groupTuple(), remainder: true )
- .join( INTEGRON_FINDER_2GFF.out.gff, remainder: true )
+ .join( ch_integron_finder_gff, remainder: true )
)
// Render reports
@@ -403,7 +408,7 @@ workflow BACANNOT {
.join( DRAW_GIS.out.example, remainder: true )
.join( phast_output_ch, remainder: true )
.join( MERGE_ANNOTATIONS.out.digis_gff )
- .join( INTEGRON_FINDER_2GFF.out.gff, remainder: true )
+ .join( ch_integron_finder_gff, remainder: true )
)
//
@@ -432,7 +437,7 @@ workflow BACANNOT {
.join( DIGIS.out.all , remainder: true )
.join( antismash_all_ch , remainder: true )
.join( MERGE_ANNOTATIONS.out.all , remainder: true )
- .join( INTEGRON_FINDER_2GFF.out.gff, remainder: true )
+ .join( ch_integron_finder_gff , remainder: true )
.join( mobsuite_output_ch , remainder: true )
)
MERGE_SUMMARIES(
@@ -440,19 +445,19 @@ workflow BACANNOT {
)
// Render circos plots
- circos_input_ch =
- annotation_out_ch.genome
- .join( annotation_out_ch.gff , remainder: true )
- .join( MERGE_ANNOTATIONS.out.gff, remainder: true )
- .join( PHISPY.out.gff , remainder: true )
- .map{
- it ->
- sample = it[0]
- it.remove(0)
- [ sample, it ]
- }
- CIRCOS(
- circos_input_ch
- )
+ if (!params.skip_circos) {
+ circos_input_ch =
+ annotation_out_ch.genome
+ .join( annotation_out_ch.gff , remainder: true )
+ .join( MERGE_ANNOTATIONS.out.gff, remainder: true )
+ .join( PHISPY.out.gff , remainder: true )
+ .map{
+ it ->
+ sample = it[0]
+ it.remove(0)
+ [ sample, it ]
+ }
+ CIRCOS( circos_input_ch )
+ }
}