Merge remote-tracking branch 'origin/main' into bd_rhapsody_sequence_…

…analysis

CHANGELOG.md

@@ -21,14 +21,29 @@
   - `seqtk/seqtk_subseq`: Extract the sequences (complete or subsequence) from the FASTA/FASTQ files
                 based on a provided sequence IDs or region coordinates file (PR #85).
 
-* `agat/agat_convert_sp_gff2gtf`: convert any GTF/GFF file into a proper GTF file (PR #76).
+* `agat`:
+  - `agat/agat_convert_sp_gff2gtf`: convert any GTF/GFF file into a proper GTF file (PR #76).
+  - `agat/agat_convert_bed2gff`: convert bed file to gff format (PR #97).
+  - `agat/agat_convert_embl2gff`: convert an EMBL file into GFF format (PR #99).
+  - `agat/agat_convert_sp_gff2tsv`: convert gtf/gff file into tabulated file (PR #102).
+  - `agat/agat_convert_sp_gxf2gxf`: fixes and/or standardizes any GTF/GFF file into full sorted GTF/GFF file (PR #103).
+
+* `bedtools`:
+  - `bedtools/bedtools_intersect`: Allows one to screen for overlaps between two sets of genomic features (PR #94).
+  - `bedtools/bedtools_sort`: Sorts a feature file (bed/gff/vcf) by chromosome and other criteria (PR #98).
+  - `bedtools/bedtools_bamtofastq`: Convert BAM alignments to FASTQ files (PR #101).
+  - `bedtools/bedtools_bedtobam`: Converts genomic feature records (bed/gff/vcf) to BAM format (PR #111).
 
 ## MINOR CHANGES
 
 * `busco` components: update BUSCO to `5.7.1` (PR #72).
 
 * Update CI to reusable workflow in `viash-io/viash-actions` (PR #86).
 
+* Update several components in order to avoid duplicate code when using `unset` on boolean arguments (PR #133).
+
+* Bump viash to `0.9.0-RC7` (PR #134)
+
 ## DOCUMENTATION
 
 * Extend the contributing guidelines (PR #82):

CONTRIBUTING.md

@@ -320,6 +320,31 @@ Notes:
 
 * If your tool allows for multiple inputs using a separator other than `;` (which is the default Viash multiple separator), you can substitute these values with a command like: `par_disable_filters=$(echo $par_disable_filters | tr ';' ',')`.
 
+* If you have a lot of boolean variables that you would like to unset when the value is `false`, you can avoid duplicate code by using the following syntax:
+
+```bash
+unset_if_false=(
+    par_argument_1
+    par_argument_2
+    par_argument_3
+    par_argument_4
+)
+
+for par in ${unset_if_false[@]}; do
+    test_val="${!par}"
+    [[ "$test_val" == "false" ]] && unset $par
+done
+```
+
+this code is equivalent to
+
+```bash
+[[ "$par_argument_1" == "false" ]] && unset par_argument_1
+[[ "$par_argument_2" == "false" ]] && unset par_argument_2
+[[ "$par_argument_3" == "false" ]] && unset par_argument_3
+[[ "$par_argument_4" == "false" ]] && unset par_argument_4
+```
+
 
 ### Step 12: Create test script
 

_viash.yaml

@@ -7,7 +7,7 @@ links:
   issue_tracker: https://github.com/viash-hub/biobox/issues
   repository: https://github.com/viash-hub/biobox
 
-viash_version: 0.9.0-RC6
+viash_version: 0.9.0-RC7
 
 config_mods: |
   .requirements.commands := ['ps']

src/agat/agat_convert_bed2gff/config.vsh.yaml

@@ -0,0 +1,86 @@
+name: agat_convert_bed2gff
+namespace: agat
+description: |
+  The script takes a bed file as input, and will translate it in gff format. The BED format is described here The script converts 0-based, half-open [start-1, end) bed file to 1-based, closed [start, end] General Feature Format v3 (GFF3).
+keywords: [gene annotations, GFF conversion]
+links:
+  homepage: https://github.com/NBISweden/AGAT
+  documentation: https://agat.readthedocs.io/en/latest/tools/agat_convert_bed2gff.html
+  issue_tracker: https://github.com/NBISweden/AGAT/issues
+  repository: https://github.com/NBISweden/AGAT
+references: 
+  doi: 10.5281/zenodo.3552717
+license: GPL-3.0
+authors:
+  - __merge__: /src/_authors/leila_paquay.yaml
+    roles: [ author, maintainer ]
+argument_groups:
+  - name: Inputs
+    arguments:
+      - name: --bed
+        description: Input bed file that will be converted.
+        type: file
+        required: true
+        direction: input
+        example: input.bed
+  - name: Outputs
+    arguments:       
+      - name: --output
+        alternatives: [-o, --out, --outfile, --gff]
+        description: Output GFF file. If no output file is specified, the output will be written to STDOUT.
+        type: file
+        direction: output
+        required: true
+        example: output.gff
+  - name: Arguments
+    arguments:
+      - name: --source
+        description: |
+          The source informs about the tool used to produce the data and is stored in 2nd field of a gff file. Example: Stringtie, Maker, Augustus, etc. [default: data]
+        type: string
+        required: false
+        example: Stringtie
+      - name: --primary_tag
+        description: |
+          The primary_tag corresponds to the data type and is stored in 3rd field of a gff file. Example: gene, mRNA, CDS, etc. [default: gene]
+        type: string
+        required: false
+        example: gene
+      - name: --inflate_off
+        description: |
+          By default we inflate the block fields (blockCount, blockSizes, blockStarts) to create subfeatures of the main feature (primary_tag). The type of subfeature created is based on the inflate_type parameter. If you do not want this inflating behaviour you can deactivate it by using the --inflate_off option.
+        type: boolean_false
+      - name: --inflate_type
+        description: |
+          Feature type (3rd column in gff) created when inflate parameter activated [default: exon].
+        type: string
+        required: false
+        example: exon
+      - name: --verbose
+        description: add verbosity
+        type: boolean_true
+      - name: --config
+        alternatives: [-c]
+        description: |
+          Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently).
+        type: file
+        required: false
+        example: custom_agat_config.yaml
+resources:
+  - type: bash_script
+    path: script.sh
+test_resources:
+  - type: bash_script
+    path: test.sh
+  - type: file
+    path: test_data
+engines:
+  - type: docker
+    image: quay.io/biocontainers/agat:1.4.0--pl5321hdfd78af_0
+    setup:
+      - type: docker
+        run: |
+          agat --version | sed 's/AGAT\s\(.*\)/agat: "\1"/' > /var/software_versions.txt
+runners:
+  - type: executable
+  - type: nextflow

src/agat/agat_convert_bed2gff/help.txt

@@ -0,0 +1,89 @@
+```sh
+agat_convert_bed2gff.pl --help
+```
+ ------------------------------------------------------------------------------
+|   Another GFF Analysis Toolkit (AGAT) - Version: v1.4.0                      |
+|   https://github.com/NBISweden/AGAT                                          |
+|   National Bioinformatics Infrastructure Sweden (NBIS) - www.nbis.se         |
+ ------------------------------------------------------------------------------
+
+
+Name:
+    agat_convert_bed2gff.pl
+
+Description:
+    The script takes a bed file as input, and will translate it in gff
+    format. The BED format is described here:
+    https://genome.ucsc.edu/FAQ/FAQformat.html#format1 The script converts
+    0-based, half-open [start-1, end) bed file to 1-based, closed [start,
+    end] General Feature Format v3 (GFF3).
+
+Usage:
+        agat_convert_bed2gff.pl --bed infile.bed [ -o outfile ]
+        agat_convert_bed2gff.pl -h
+
+Options:
+    --bed   Input bed file that will be converted.
+
+    --source
+            The source informs about the tool used to produce the data and
+            is stored in 2nd field of a gff file. Example:
+            Stringtie,Maker,Augustus,etc. [default: data]
+
+    --primary_tag
+            The primary_tag corresponds to the data type and is stored in
+            3rd field of a gff file. Example: gene,mRNA,CDS,etc. [default:
+            gene]
+
+    --inflate_off
+            By default we inflate the block fields (blockCount, blockSizes,
+            blockStarts) to create subfeatures of the main feature
+            (primary_tag). The type of subfeature created is based on the
+            inflate_type parameter. If you do not want this inflating
+            behaviour you can deactivate it by using the --inflate_off
+            option.
+
+    --inflate_type
+            Feature type (3rd column in gff) created when inflate parameter
+            activated [default: exon].
+
+    --verbose
+            add verbosity
+
+    -o , --output , --out , --outfile or --gff
+            Output GFF file. If no output file is specified, the output will
+            be written to STDOUT.
+
+    -c or --config
+            String - Input agat config file. By default AGAT takes as input
+            agat_config.yaml file from the working directory if any,
+            otherwise it takes the orignal agat_config.yaml shipped with
+            AGAT. To get the agat_config.yaml locally type: "agat config
+            --expose". The --config option gives you the possibility to use
+            your own AGAT config file (located elsewhere or named
+            differently).
+
+    -h or --help
+            Display this helpful text.
+
+Feedback:
+  Did you find a bug?:
+    Do not hesitate to report bugs to help us keep track of the bugs and
+    their resolution. Please use the GitHub issue tracking system available
+    at this address:
+
+                https://github.com/NBISweden/AGAT/issues
+
+     Ensure that the bug was not already reported by searching under Issues.
+     If you're unable to find an (open) issue addressing the problem, open a new one.
+     Try as much as possible to include in the issue when relevant:
+     - a clear description,
+     - as much relevant information as possible,
+     - the command used,
+     - a data sample,
+     - an explanation of the expected behaviour that is not occurring.
+
+  Do you want to contribute?:
+    You are very welcome, visit this address for the Contributing
+    guidelines:
+    https://github.com/NBISweden/AGAT/blob/master/CONTRIBUTING.md

src/agat/agat_convert_bed2gff/script.sh

@@ -0,0 +1,19 @@
+#!/bin/bash
+
+## VIASH START
+## VIASH END
+
+# unset flags
+[[ "$par_inflate_off" == "true" ]] && unset par_inflate_off
+[[ "$par_verbose" == "false" ]] && unset par_verbose
+
+# run agat_convert_sp_bed2gff.pl
+agat_convert_bed2gff.pl \
+  --bed "$par_bed" \
+  -o "$par_output" \
+  ${par_source:+--source "${par_source}"} \
+  ${par_primary_tag:+--primary_tag "${par_primary_tag}"} \
+  ${par_inflate_off:+--inflate_off} \
+  ${par_inflate_type:+--inflate_type "${par_inflate_type}"} \
+  ${par_verbose:+--verbose}
+  ${par_config:+--config "${par_config}"} \

src/agat/agat_convert_bed2gff/test.sh

@@ -0,0 +1,27 @@
+#!/bin/bash
+
+## VIASH START
+## VIASH END
+
+test_dir="${meta_resources_dir}/test_data"
+out_dir="${meta_resources_dir}/out_data"
+
+echo "> Run $meta_name with test data"
+"$meta_executable" \
+  --bed "$test_dir/test.bed" \
+  --output "$out_dir/output.gff" 
+
+echo ">> Checking output"
+[ ! -f "$out_dir/output.gff" ] && echo "Output file output.gff does not exist" && exit 1
+
+echo ">> Check if output is empty"
+[ ! -s "$out_dir/output.gff" ] && echo "Output file output.gff is empty" && exit 1
+
+echo ">> Check if output matches expected output"
+diff "$out_dir/output.gff" "$test_dir/agat_convert_bed2gff_1.gff"
+if [ $? -ne 0 ]; then
+  echo "Output file output.gff does not match expected output"
+  exit 1
+fi
+
+echo "> Test successful"

src/agat/agat_convert_bed2gff/test_data/agat_convert_bed2gff_1.gff

@@ -0,0 +1,12 @@
+##gff-version 3
+scaffold625	data	gene	337818	343277	.	+	.	ID=1;Name=CLUHART00000008717;blockCount=4;blockSizes=154%2C109%2C111%2C1314;blockStarts=0%2C2915%2C3700%2C4146;itemRgb=255%2C0%2C0;thickEnd=343033;thickStart=337914
+scaffold625	data	exon	337818	337971	.	+	.	ID=exon1;Parent=1
+scaffold625	data	exon	340733	340841	.	+	.	ID=exon2;Parent=1
+scaffold625	data	exon	341518	341628	.	+	.	ID=exon3;Parent=1
+scaffold625	data	exon	341964	343277	.	+	.	ID=exon4;Parent=1
+scaffold625	data	CDS	337915	337971	.	+	0	ID=CDS1;Parent=1
+scaffold625	data	CDS	340733	340841	.	+	0	ID=CDS2;Parent=1
+scaffold625	data	CDS	341518	341628	.	+	2	ID=CDS3;Parent=1
+scaffold625	data	CDS	341964	343033	.	+	2	ID=CDS4;Parent=1
+scaffold625	data	five_prime_UTR	337818	337914	.	+	.	ID=five_prime_UTR1;Parent=1
+scaffold625	data	three_prime_UTR	343034	343277	.	+	.	ID=three_prime_UTR1;Parent=1

src/agat/agat_convert_bed2gff/test_data/script.sh

@@ -0,0 +1,10 @@
+#!/bin/bash
+
+# clone repo
+if [ ! -d /tmp/agat_source ]; then
+  git clone --depth 1 --single-branch --branch master https://github.com/NBISweden/AGAT /tmp/agat_source
+fi
+
+# copy test data
+cp -r /tmp/agat_source/t/scripts_output/in/test.bed src/agat/agat_convert_bed2gff/test_data/test.bed
+cp -r /tmp/agat_source/t/scripts_output/out/agat_convert_bed2gff_1.gff src/agat/agat_convert_bed2gff/test_data/agat_convert_bed2gff_1.gff

src/agat/agat_convert_bed2gff/test_data/test.bed

@@ -0,0 +1 @@
+scaffold625	337817	343277	CLUHART00000008717	0	+	337914	343033	255,0,0	4	154,109,111,1314	0,2915,3700,4146