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add support for Cascadia search engine
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,193 @@ | ||
| process CASCADIA_SEARCH { | ||
| publishDir params.output_directories.cascadia, failOnError: true, mode: 'copy' | ||
| label 'process_high_constant' | ||
| container params.images.cascadia | ||
|
|
||
| containerOptions = { | ||
|
|
||
| def options = '' | ||
| if (params.cascadia.use_gpu) { | ||
| if (workflow.containerEngine == "singularity" || workflow.containerEngine == "apptainer") { | ||
| options += ' --nv' | ||
| } else if (workflow.containerEngine == "docker") { | ||
| options += ' --gpus all' | ||
| } | ||
| } | ||
|
|
||
| return options | ||
| } | ||
|
|
||
| // don't melt the GPU | ||
| if (params.cascadia.use_gpu) { | ||
| maxForks = 1 | ||
| } | ||
|
|
||
| input: | ||
| path ms_file | ||
|
|
||
| output: | ||
| path("*.stderr"), emit: stderr | ||
| path("*.stdout"), emit: stdout | ||
| tuple(path(ms_file), path("${ms_file.baseName}.ssl"), emit: ssl) | ||
| path("${ms_file.baseName}.ssl"), emit: published_ssl | ||
| path("cascadia_version.txt"), emit: version | ||
| path("output_file_stats_${ms_file.baseName}.txt"), emit: output_file_stats | ||
|
|
||
| script: | ||
|
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| """ | ||
| cascadia sequence ${ms_file} /usr/local/bin/cascadia.ckpt --out ${ms_file.baseName} | ||
| > >(tee "${ms_file.baseName}.stdout") 2> >(tee "${ms_file.baseName}.stderr" >&2) | ||
| echo "${params.images.cascadia}" | egrep -o '[0-9]+\\.[0-9]+\\.[0-9]+' | xargs printf "cascadia_version=%s\n" > cascadia_version.txt | ||
| md5sum '${ms_file.join('\' \'')}' ${ms_file.baseName}.ssl | sed -E 's/([a-f0-9]{32}) [ \\*](.*)/\\2\\t\\1/' | sort > hashes.txt | ||
| stat -L --printf='%n\t%s\n' '${ms_file.join('\' \'')}' ${ms_file.baseName}.ssl | sort > sizes.txt | ||
| join -t'\t' hashes.txt sizes.txt > output_file_stats_${ms_file.baseName}.txt | ||
| """ | ||
|
|
||
| stub: | ||
| """ | ||
| touch stub.ssl | ||
| touch stub.stderr stub.stdout | ||
| echo "${params.images.cascadia}" | egrep -o '[0-9]+\\.[0-9]+\\.[0-9]+' | xargs printf "cascadia_version=%s\n" > cascadia_version.txt | ||
| md5sum '${ms_file.join('\' \'')}' stub.ssl | sed -E 's/([a-f0-9]{32}) [ \\*](.*)/\\2\\t\\1/' | sort > hashes.txt | ||
| stat -L --printf='%n\t%s\n' '${ms_file.join('\' \'')}' stub.ssl | sort > sizes.txt | ||
| join -t'\t' hashes.txt sizes.txt > output_file_stats_${ms_file.baseName}.txt | ||
| """ | ||
| } | ||
|
|
||
| process CASCADIA_FIX_SCAN_NUMBERS { | ||
| publishDir params.output_directories.cascadia, failOnError: true, mode: 'copy' | ||
| label 'process_medium' | ||
| container params.images.cascadia_utils | ||
|
|
||
| input: | ||
| tuple path(ms_file), path(ssl_file) | ||
|
|
||
| output: | ||
| path("*.stderr"), emit: stderr | ||
| path("*.stdout"), emit: stdout | ||
| path("${ssl_file.baseName}.fixed.ssl"), emit: fixed_ssl | ||
| path("cascadia-utils_version.txt"), emit: version | ||
| path("output_file_stats.txt"), emit: output_file_stats | ||
|
|
||
| script: | ||
|
|
||
| """ | ||
| python3 /usr/local/bin/fix_scan_numbers.py ${ssl_file} ${ms_file} ${ssl_file.baseName}.fixed.ssl | ||
| > >(tee "fix_scan_numbers.stdout") 2> >(tee "fix_scan_numbers.stderr" >&2) | ||
| echo "${params.images.cascadia_utils}" | egrep -o '[0-9]+\\.[0-9]+\\.[0-9]+' | xargs printf "cascadia-utils_version=%s\n" > cascadia-utils_version.txt | ||
| md5sum ${ms_file} ${ssl_file} ${ssl_file.baseName}.fixed.ssl | sed -E 's/([a-f0-9]{32}) [ \\*](.*)/\\2\\t\\1/' | sort > hashes.txt | ||
| stat -L --printf='%n\t%s\n' ${ms_file} ${ssl_file} ${ssl_file.baseName}.fixed.ssl | sort > sizes.txt | ||
| join -t'\t' hashes.txt sizes.txt > output_file_stats.txt | ||
| """ | ||
|
|
||
| stub: | ||
| """ | ||
| touch stub.fixed.ssl | ||
| echo "${params.images.cascadia_utils}" | egrep -o '[0-9]+\\.[0-9]+\\.[0-9]+' | xargs printf "cascadia-utils_version=%s\n" > cascadia-utils_version.txt | ||
| md5sum ${ms_file} ${ssl_file} stub.fixed.ssl | sed -E 's/([a-f0-9]{32}) [ \\*](.*)/\\2\\t\\1/' | sort > hashes.txt | ||
| stat -L --printf='%n\t%s\n' ${ms_file} ${ssl_file} stub.fixed.ssl | sort > sizes.txt | ||
| join -t'\t' hashes.txt sizes.txt > output_file_stats.txt | ||
| """ | ||
| } | ||
|
|
||
| process CASCADIA_CREATE_FASTA { | ||
| publishDir params.output_directories.cascadia, failOnError: true, mode: 'copy' | ||
| label 'process_medium' | ||
| container params.images.cascadia_utils | ||
|
|
||
| input: | ||
| path ssl_file | ||
|
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||
| output: | ||
| path("*.stderr"), emit: stderr | ||
| path("*.stdout"), emit: stdout | ||
| path("${ssl_file.baseName}.fasta"), emit: fasta | ||
| path("cascadia-utils_version.txt"), emit: version | ||
| path("output_file_stats.txt"), emit: output_file_stats | ||
|
|
||
| script: | ||
|
|
||
| """ | ||
| python3 /usr/local/bin/create_fasta_from_ssl.py ${ssl_file} ${ssl_file.baseName}.fasta | ||
| > >(tee "create_fasta.stdout") 2> >(tee "create_fasta.stderr" >&2) | ||
| echo "${params.images.cascadia_utils}" | egrep -o '[0-9]+\\.[0-9]+\\.[0-9]+' | xargs printf "cascadia-utils_version=%s\n" > cascadia-utils_version.txt | ||
| md5sum ${ssl_file} ${ssl_file.baseName}.fasta | sed -E 's/([a-f0-9]{32}) [ \\*](.*)/\\2\\t\\1/' | sort > hashes.txt | ||
| stat -L --printf='%n\t%s\n' ${ssl_file} ${ssl_file.baseName}.fasta | sort > sizes.txt | ||
| join -t'\t' hashes.txt sizes.txt > output_file_stats.txt | ||
| """ | ||
|
|
||
| stub: | ||
| """ | ||
| touch stub.ssl stub.fasta | ||
| echo "${params.images.cascadia_utils}" | egrep -o '[0-9]+\\.[0-9]+\\.[0-9]+' | xargs printf "cascadia-utils_version=%s\n" > cascadia-utils_version.txt | ||
| md5sum stub.ssl stub.fasta | sed -E 's/([a-f0-9]{32}) [ \\*](.*)/\\2\\t\\1/' | sort > hashes.txt | ||
| stat -L --printf='%n\t%s\n' stub.ssl stub.fasta | sort > sizes.txt | ||
| join -t'\t' hashes.txt sizes.txt > output_file_stats.txt | ||
| """ | ||
| } | ||
|
|
||
| process CASCADIA_COMBINE_SSL_FILES { | ||
| publishDir params.output_directories.cascadia, failOnError: true, mode: 'copy' | ||
| label 'process_medium' | ||
| container params.images.cascadia_utils | ||
|
|
||
| input: | ||
| path ssl_files | ||
|
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||
| output: | ||
| path("combined.ssl"), emit: ssl | ||
| path("output_file_stats.txt"), emit: output_file_stats | ||
|
|
||
| script: | ||
|
|
||
| """ | ||
| python3 /usr/local/bin/combine_ssl_files.py *.ssl > combined.ssl | ||
| md5sum '${ssl_files.join('\' \'')}' combined.ssl | sed -E 's/([a-f0-9]{32}) [ \\*](.*)/\\2\\t\\1/' | sort > hashes.txt | ||
| stat -L --printf='%n\t%s\n' '${ssl_files.join('\' \'')}' combined.ssl | sort > sizes.txt | ||
| join -t'\t' hashes.txt sizes.txt > output_file_stats.txt | ||
| """ | ||
|
|
||
| stub: | ||
| """ | ||
| touch combined.ssl | ||
| md5sum '${ssl_files.join('\' \'')}' combined.ssl | sed -E 's/([a-f0-9]{32}) [ \\*](.*)/\\2\\t\\1/' | sort > hashes.txt | ||
| stat -L --printf='%n\t%s\n' '${ssl_files.join('\' \'')}' combined.ssl | sort > sizes.txt | ||
| join -t'\t' hashes.txt sizes.txt > output_file_stats.txt | ||
| """ | ||
| } | ||
|
|
||
| process BLIB_BUILD_LIBRARY { | ||
| publishDir params.output_directories.cascadia, failOnError: true, mode: 'copy' | ||
| label 'process_medium' | ||
| container params.images.bibliospec | ||
|
|
||
| input: | ||
| path ssl | ||
| path mzml_files | ||
|
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||
| output: | ||
| path('lib.blib'), emit: blib | ||
|
|
||
| script: | ||
| """ | ||
| BlibBuild "${ssl}" lib_redundant.blib | ||
| BlibFilter -b 1 lib_redundant.blib lib.blib | ||
| """ | ||
|
|
||
| stub: | ||
| """ | ||
| touch lib.blib | ||
| """ | ||
| } |
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