Merge pull request #4 from viash-hub/add_bgzip

Add bgzip

src/bgzip/config.vsh.yaml

@@ -0,0 +1,124 @@
+functionality:
+  name: bgzip
+  description: Block compression/decompression utility
+  info:
+    homepage: https://www.htslib.org/
+    documentation: https://www.htslib.org/doc/bgzip.html
+    repository: https://github.com/samtools/htslib
+    licence: MIT
+  requirements:
+    cpus: 1
+    commands: [ bgzip ]
+  argument_groups:
+    - name: Inputs
+      arguments:
+      - name: --input
+        type: file
+        direction: input
+        description: file to be compressed or decompressed
+        required: true
+    - name: Outputs
+      arguments:
+      - name: --output
+        type: file
+        direction: output
+        description: compressed or decompressed output
+        required: true
+      - name: --index_name
+        alternatives: -I
+        type: file
+        direction: output
+        description: name of BGZF index file [file.gz.gzi]
+    - name: Arguments
+      arguments:
+      - name: offset
+        alternatives: -b
+        type: integer
+        description: decompress at virtual file pointer (0-based uncompressed offset)
+      - name: --decompress
+        alternatives: -d
+        type: boolean_true
+        description: decompress the input file
+      - name: --rebgzip
+        alternatives: -g
+        type: boolean_true
+        description: use an index file to bgzip a file
+      - name: --index
+        alternatives: -i
+        type: boolean_true
+        description: compress and create BGZF index
+      - name: --compress_level
+        alternatives: -l
+        type: integer
+        description: compression level to use when compressing; 0 to 9, or -1 for default [-1]
+        min: -1
+        max: 9
+      - name: --reindex
+        alternatives: -r
+        type: boolean_true
+        description: (re)index the output file
+      - name: --size
+        alternatives: -s
+        type: integer
+        description: decompress INT bytes (uncompressed size)
+        min: 0
+      - name: --test
+        alternatives: -t
+        type: boolean_true
+        description: test integrity of compressed file
+      - name: --binary
+        type: boolean_true
+        description: Don't align blocks with text lines
+  resources:
+    - type: bash_script
+      text: |
+        [[ "$par_decompress" == "false" ]] && unset par_decompress
+        [[ "$par_rebgzip" == "false" ]] && unset par_rebgzip
+        [[ "$par_index" == "false" ]] && unset par_index
+        [[ "$par_reindex" == "false" ]] && unset par_reindex
+        [[ "$par_test" == "false" ]] && unset par_test
+        [[ "$par_binary" == "false" ]] && unset par_binary
+        bgzip -c \
+          ${meta_cpus:+--threads "${meta_cpus}"} \
+          ${par_decompress:+-d} \
+          ${par_rebgzip:+-g} \
+          ${par_index:+-i} \
+          ${par_index_name:+-I "${par_index_name}"} \
+          ${par_compress_level:+-l "${par_compress_level}"} \
+          ${par_reindex:+-r} \
+          ${par_size:+-s "${par_size}"} \
+          ${par_test:+-t} \
+          "$par_input" > "$par_output"
+  test_resources:
+    - type: bash_script
+      text: |
+        set -e
+
+        "$meta_executable" --input "$meta_resources_dir/test_data/test.vcf" --output "test.vcf.gz"
+
+        echo ">> Checking output of compressing"
+        [ ! -f "test.vcf.gz" ] && echo "Output file test.vcf.gz does not exist" && exit 1
+
+        "$meta_executable" --input "test.vcf.gz" --output "test.vcf" --decompress
+
+        echo ">> Checking output of decompressing"
+        [ ! -f "test.vcf" ] && echo "Output file test.vcf does not exist" && exit 1
+
+        echo ">> Checking original and decompressed files are the same"
+        set +e
+        cmp --silent -- "$meta_resources_dir/test_data/test.vcf" "test.vcf"
+        [ $? -ne 0 ] && echo "files are different" && exit 1
+        set -e
+        
+        echo "> Test successful"
+    - type: file
+      path: test_data
+
+platforms:
+  - type: docker
+    image: quay.io/biocontainers/htslib:1.19--h81da01d_0
+    setup:
+      - type: docker
+        run: |
+          bgzip -h | grep 'Version:' 2>&1 |  sed 's/Version:\s\(.*\)/arriba: "\1"/' > /var/software_versions.txt
+  - type: nextflow

src/bgzip/help.txt

@@ -0,0 +1,22 @@
+```bash
+bgzip -h
+```
+
+Version: 1.19
+Usage:   bgzip [OPTIONS] [FILE] ...
+Options:
+   -b, --offset INT           decompress at virtual file pointer (0-based uncompressed offset)
+   -c, --stdout               write on standard output, keep original files unchanged
+   -d, --decompress           decompress
+   -f, --force                overwrite files without asking
+   -g, --rebgzip              use an index file to bgzip a file
+   -h, --help                 give this help
+   -i, --index                compress and create BGZF index
+   -I, --index-name FILE      name of BGZF index file [file.gz.gzi]
+   -k, --keep                 don't delete input files during operation
+   -l, --compress-level INT   Compression level to use when compressing; 0 to 9, or -1 for default [-1]
+   -r, --reindex              (re)index compressed file
+   -s, --size INT             decompress INT bytes (uncompressed size)
+   -t, --test                 test integrity of compressed file
+       --binary               Don't align blocks with text lines
+   -@, --threads INT          number of compression threads to use [1]

src/bgzip/test_data/README.md

@@ -0,0 +1,13 @@
+# arriba test data
+
+Test data was obtained from https://github.com/snakemake/snakemake-wrappers/tree/master/bio/bgzip/test.
+
+__author__ = "William Rowell"
+__copyright__ = "Copyright 2020, William Rowell"
+__email__ = "[email protected]"
+__license__ = "MIT"
+
+```bash
+git clone --depth 1 --single-branch --branch master https://github.com/snakemake/snakemake-wrappers /tmp/snakemake-wrappers
+cp -r /tmp/snakemake-wrappers/bio/bgzip/test/* src/bgzip/test_data
+```

src/bgzip/test_data/test.vcf

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+##fileformat=VCFv4.0
+##fileDate=20090805
+##source=https://www.internationalgenome.org/wiki/Analysis/vcf4.0/
+##reference=1000GenomesPilot-NCBI36
+##phasing=partial
+##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
+##INFO=<ID=AF,Number=.,Type=Float,Description="Allele Frequency">
+##INFO=<ID=AA,Number=1,Type=String,Description="Ancestral Allele">
+##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP membership, build 129">
+##INFO=<ID=H2,Number=0,Type=Flag,Description="HapMap2 membership">
+##FILTER=<ID=q10,Description="Quality below 10">
+##FILTER=<ID=s50,Description="Less than 50% of samples have data">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
+##FORMAT=<ID=HQ,Number=2,Type=Integer,Description="Haplotype Quality">
+#CHROM POS     ID        REF ALT    QUAL FILTER INFO                              FORMAT      NA00001        NA00002        NA00003
+20     14370   rs6054257 G      A       29   PASS   NS=3;DP=14;AF=0.5;DB;H2           GT:GQ:DP:HQ 0|0:48:1:51,51 1|0:48:8:51,51 1/1:43:5:.,.
+20     17330   .         T      A       3    q10    NS=3;DP=11;AF=0.017               GT:GQ:DP:HQ 0|0:49:3:58,50 0|1:3:5:65,3   0/0:41:3
+20     1110696 rs6040355 A      G,T     67   PASS   NS=2;DP=10;AF=0.333,0.667;AA=T;DB GT:GQ:DP:HQ 1|2:21:6:23,27 2|1:2:0:18,2   2/2:35:4
+20     1230237 .         T      .       47   PASS   NS=3;DP=13;AA=T                   GT:GQ:DP:HQ 0|0:54:7:56,60 0|0:48:4:51,51 0/0:61:2
+20     1234567 microsat1 GTCT   G,GTACT 50   PASS   NS=3;DP=9;AA=G                    GT:GQ:DP    0/1:35:4       0/2:17:2       1/1:40:3