Initial commit index component

src/samtools/index/config.vsh.yaml

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+name: samtools_index
+namespace: samtools
+description: Index BAM files
+keywords: [stats, mapping, counts, chromosome, bam, sam, cram]
+links:
+  homepage: https://www.htslib.org/
+  documentation: https://www.htslib.org/doc/samtools-index.html
+  repository: https://github.com/samtools/samtools.git
+references: 
+  doi: 10.1093/bioinformatics/btp352, 10.1093/gigascience/giab008
+license: MIT/Expat
+
+argument_groups:
+  - name: Inputs
+    arguments:
+      - name: --bam
+        alternatives: -b
+        type: file
+        description: BAM input file.
+      - name: "--bam_csi_index"
+        type: boolean
+        description: Create a CSI index for BAM files instead of the traditional BAI index. This will be required for genomes with larger chromosome sizes.
+  - name: Outputs
+    arguments:
+      - name: --output_bai
+        alternatives: [ -o, --output ]
+        type: file
+        description: BAM index
+        direction: output
+        required: true
+        must_exist: false
+        example: out.bam.bai
+        must_exist: false
+      - name: --output_csi
+        alternatives: [ -c, --csi ]
+        type: file
+        description: CSI index
+        direction: output
+        default: out.bam.csi
+      - name: --min-shift
+        alternatives: -m
+        type: integer
+        description: Create a CSI index, with a minimum interval size of 2^INT.
+        default: 0
+  - name: Options
+    arguments:
+      - name: --individual
+        alternatives: -M
+        type: integer
+        description: |
+          Interpret all filename arguments as alignment files to
+          be indexed individually. (Without -M, filename arguments
+          are interpreted solely as per the second synopsis.)
+
+
+   
+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/samtools:1.19.2--h50ea8bc_1
+    setup:
+      - type: docker
+        run: |
+          echo "$(samtools --version 2>&1)" > /var/software_versions.txt
+runners:
+- type: executable
+- type: nextflow

src/samtools/index/help.txt

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+```
+samtools index
+```
+
+Usage: samtools index [-bc] [-m INT] <in.bam> [out.index]
+Options:
+  -b       Generate BAI-format index for BAM files [default]
+  -c       Generate CSI-format index for BAM files
+  -m INT   Set minimum interval size for CSI indices to 2^INT [14]

src/samtools/index/script.sh

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+#!/bin/bash
+
+## VIASH START
+## VIASH END
+
+set -e
+
+[[ "$par_output_csi" == "false" ]] && unset par_output_csi
+
+samtools index \
+    "$par_input" \
+    ${par_output_csi:+-c} \
+    -o "$par_output"

src/samtools/index/test.sh

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+#!/bin/bash
+
+test_dir="${meta_resources_dir}test_data"
+echo ">>> Testing $meta_functionality_name"
+
+echo ">>> Generating BAM index"
+"$meta_executable" \
+  --input "$test_dir/chr19.bam" \
+  --bam_csi_index false \
+  --output_bai "$test_dir/chr19.bam.bai"
+
+echo ">>> Check whether output exists"
+[ ! -f chr19.bam.bai ] && echo "File 'mapt.NA12156.altex.bam.bai' does not exist!" && exit 1
+[ ! -s chr19.bam.bai ] && echo "File 'mapt.NA12156.altex.bam.bai' is empty!" && exit 1
+
+echo ">>> Generating CSI index"
+"$meta_executable" \
+  --input "$test_dir/chr19.bam" \
+  --bam_csi_index true \
+  --output_csi "$test_dir/chr19.bam.csi"
+
+echo ">>> Check whether output exists"
+[ ! -f "chr19.bam.csi" ] && echo "File 'mapt.NA12156.altex.bam.csi' does not exist!" && exit 1
+[ ! -s "chr19.bam.csi" ] && echo "File 'mapt.NA12156.altex.bam.csi' is empty!" && exit 1
+
+echo "All tests succeeded!"
+exit 0

src/samtools/index/test_data/script.sh

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+#!/bin/bash
+
+# dowload test data from snakemake wrapper
+if [ ! -d /tmp/idxstats_source ]; then
+  git clone --depth 1 --single-branch --branch master https://github.com/snakemake/snakemake-wrappers.git /tmp/idxstats_source
+fi
+
+cp -r /tmp/idxstats_source/bio/samtools/idxstats/test/mapped/* src/samtools/idxstats/test_data
+# samtools idxstats a.sorted.bam > a.sorted.idxstats
+
+# dowload test data from nf-core module
+wget https://github.com/nf-core/test-datasets/raw/modules/data/genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam
+wget https://github.com/nf-core/test-datasets/raw/modules/data/genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai
+# samtools idxstats test.paired_end.sorted.bam > test_ref.paired_end.sorted.idxstats