diff --git a/src/bgzip/config.vsh.yaml b/src/bgzip/config.vsh.yaml deleted file mode 100644 index 26e31ae4..00000000 --- a/src/bgzip/config.vsh.yaml +++ /dev/null @@ -1,128 +0,0 @@ -name: bgzip -description: Block compression/decompression utility -links: - homepage: https://www.htslib.org/ - documentation: https://www.htslib.org/doc/bgzip.html - repository: https://github.com/samtools/htslib -references: - doi: 10.1093/gigascience/giab007 -license: MIT -requirements: - 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}"} \ - ${par_offset:+-b "${par_offset}"} \ - ${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} \ - ${par_binary:+--binary} \ - "$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 - -engines: - - 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\(.*\)/bgzip: "\1"/' > /var/software_versions.txt -runners: - - type: executable - - type: nextflow \ No newline at end of file diff --git a/src/bgzip/help.txt b/src/bgzip/help.txt deleted file mode 100644 index d4012efd..00000000 --- a/src/bgzip/help.txt +++ /dev/null @@ -1,22 +0,0 @@ -```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] diff --git a/src/bgzip/test_data/script.sh b/src/bgzip/test_data/script.sh deleted file mode 100644 index c9114473..00000000 --- a/src/bgzip/test_data/script.sh +++ /dev/null @@ -1,10 +0,0 @@ -# bgzip test data - -# Test data was obtained from https://github.com/snakemake/snakemake-wrappers/tree/master/bio/bgzip/test. - -if [ ! -d /tmp/snakemake-wrappers ]; then - git clone --depth 1 --single-branch --branch master https://github.com/snakemake/snakemake-wrappers /tmp/snakemake-wrappers -fi - -cp -r /tmp/snakemake-wrappers/bio/bgzip/test/* src/bgzip/test_data - diff --git a/src/bgzip/test_data/test.vcf b/src/bgzip/test_data/test.vcf deleted file mode 100644 index 11b5400e..00000000 --- a/src/bgzip/test_data/test.vcf +++ /dev/null @@ -1,23 +0,0 @@ -##fileformat=VCFv4.0 -##fileDate=20090805 -##source=https://www.internationalgenome.org/wiki/Analysis/vcf4.0/ -##reference=1000GenomesPilot-NCBI36 -##phasing=partial -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##FILTER= -##FILTER= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -#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