Bedtools bamtobed (#109)

* adding back my work

* adding more tests

- fixing bug
- more tests

* Final test added

* Update CHANGELOG.md

* minor change

- license name
- help file

* small changes on config

* small changes

* adding more links

* Update script.sh

* Adding $TMPDIR to test.sh

---------

Co-authored-by: Emma Rousseau <[email protected]>
Co-authored-by: Robrecht Cannoodt <[email protected]>

CHANGELOG.md

@@ -11,10 +11,14 @@
 
 * `bd_rhapsody/bd_rhapsody_sequence_analysis`: BD Rhapsody Sequence Analysis CWL pipeline (PR #96).
 
+* `bedtools`:
+   - `bedtools/bedtools_bamtobed`: Converts BAM alignments to BED6 or BEDPE format (PR #109).
+
 * `rsem/rsem_calculate_expression`: Calculate expression levels (PR #93).
 
 * `nanoplot`: Plotting tool for long read sequencing data and alignments (PR #95).
 
+
 ## BREAKING CHANGES
 
 * `falco`: Fix a typo in the `--reverse_complement` argument (PR #157).

src/bedtools/bedtools_bamtobed/config.vsh.yaml

@@ -0,0 +1,118 @@
+name: bedtools_bamtobed
+namespace: bedtools
+description: Converts BAM alignments to BED6 or BEDPE format.
+keywords: [Converts, BAM, BED, BED6, BEDPE]
+links:
+  documentation: https://bedtools.readthedocs.io/en/latest/content/tools/bamtobed.html
+  repository: https://github.com/arq5x/bedtools2
+  homepage: https://bedtools.readthedocs.io/en/latest/#
+  issue_tracker: https://github.com/arq5x/bedtools2/issues
+references:
+  doi: 10.1093/bioinformatics/btq033
+license: MIT
+requirements:
+  commands: [bedtools]
+authors:
+  - __merge__: /src/_authors/theodoro_gasperin.yaml
+    roles: [ author, maintainer ]
+
+argument_groups:
+  - name: Inputs
+    arguments:
+      - name: --input
+        alternatives: -i
+        type: file
+        description: Input BAM file.
+        required: true
+
+  - name: Outputs
+    arguments:
+      - name: --output
+        alternatives: -o
+        required: true
+        type: file
+        direction: output
+        description: Output BED file.
+
+  - name: Options
+    arguments:
+      - name: --bedpe
+        type: boolean_true
+        description: | 
+          Write BEDPE format. Requires BAM to be grouped or sorted by query.
+      
+      - name: --mate1
+        type: boolean_true
+        description: | 
+          When writing BEDPE (-bedpe) format, always report mate one as the first BEDPE "block".
+      
+      - name: --bed12
+        type: boolean_true
+        description: | 
+          Write "blocked" BED format (aka "BED12"). Forces -split.
+          See http://genome-test.cse.ucsc.edu/FAQ/FAQformat#format1
+
+      - name: --split
+        type: boolean_true
+        description: | 
+          Report "split" BAM alignments as separate BED entries.
+          Splits only on N CIGAR operations.
+
+      - name: --splitD
+        type: boolean_true
+        description: | 
+          Split alignments based on N and D CIGAR operators.
+          Forces -split.
+
+      - name: --edit_distance
+        alternatives: -ed
+        type: boolean_true
+        description: | 
+          Use BAM edit distance (NM tag) for BED score.
+          - Default for BED is to use mapping quality.
+          - Default for BEDPE is to use the minimum of
+            the two mapping qualities for the pair.
+          - When -ed is used with -bedpe, the total edit
+            distance from the two mates is reported.
+
+      - name: --tag
+        type: string
+        description: | 
+          Use other NUMERIC BAM alignment tag for BED score.
+          Default for BED is to use mapping quality. Disallowed with BEDPE output.
+        example: "SM"
+
+      - name: --color
+        type: string
+        description: | 
+          An R,G,B string for the color used with BED12 format.
+          Default is (255,0,0).
+        example: "250,250,250"
+
+      - name: --cigar
+        type: boolean_true
+        description: | 
+          Add the CIGAR string to the BED entry as a 7th column.
+
+resources:
+  - type: bash_script
+    path: script.sh
+
+test_resources:
+  - type: bash_script
+    path: test.sh
+  - path: test_data
+
+engines:
+  - type: docker
+    image: debian:stable-slim
+    setup:
+      - type: apt
+        packages: [bedtools, procps]
+      - type: docker
+        run: |
+          echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var/software_versions.txt
+
+runners:
+  - type: executable
+  - type: nextflow

src/bedtools/bedtools_bamtobed/help.txt

@@ -0,0 +1,43 @@
+```bash
+bedtools bamtobed
+```
+
+Tool:    bedtools bamtobed (aka bamToBed)
+Version: v2.30.0
+Summary: Converts BAM alignments to BED6 or BEDPE format.
+
+Usage:   bedtools bamtobed [OPTIONS] -i <bam> 
+
+Options: 
+	-bedpe	Write BEDPE format.
+		- Requires BAM to be grouped or sorted by query.
+
+	-mate1	When writing BEDPE (-bedpe) format, 
+		always report mate one as the first BEDPE "block".
+
+	-bed12	Write "blocked" BED format (aka "BED12"). Forces -split.
+
+		http://genome-test.cse.ucsc.edu/FAQ/FAQformat#format1
+
+	-split	Report "split" BAM alignments as separate BED entries.
+		Splits only on N CIGAR operations.
+
+	-splitD	Split alignments based on N and D CIGAR operators.
+		Forces -split.
+
+	-ed	Use BAM edit distance (NM tag) for BED score.
+		- Default for BED is to use mapping quality.
+		- Default for BEDPE is to use the minimum of
+		  the two mapping qualities for the pair.
+		- When -ed is used with -bedpe, the total edit
+		  distance from the two mates is reported.
+
+	-tag	Use other NUMERIC BAM alignment tag for BED score.
+		- Default for BED is to use mapping quality.
+		  Disallowed with BEDPE output.
+
+	-color	An R,G,B string for the color used with BED12 format.
+		Default is (255,0,0).
+
+	-cigar	Add the CIGAR string to the BED entry as a 7th column.
+

src/bedtools/bedtools_bamtobed/script.sh

@@ -0,0 +1,39 @@
+#!/bin/bash
+
+## VIASH START
+## VIASH END
+
+set -eo pipefail
+
+# Unset parameters
+unset_if_false=( 
+  par_bedpe
+  par_mate1
+  par_bed12
+  par_split
+  par_splitD
+  par_edit_distance
+  par_tag
+  par_color
+  par_cigar
+)
+
+for par in ${unset_if_false[@]}; do
+    test_val="${!par}"
+    [[ "$test_val" == "false" ]] && unset $par
+done
+
+# Execute bedtools sort with the provided arguments
+bedtools bamtobed \
+    ${par_bedpe:+-bedpe} \
+    ${par_mate1:+-mate1} \
+    ${par_bed12:+-bed12} \
+    ${par_split:+-split} \
+    ${par_splitD:+-splitD} \
+    ${par_edit_distance:+-ed} \
+    ${par_tag:+-tag "$par_tag"} \
+    ${par_cigar:+-cigar} \
+    ${par_color:+-color "$par_color"} \
+    -i "$par_input" \
+    > "$par_output"
+