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https://github.com/MillironX/nf-core_modules.git
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b4452a4881
* first commit * entrezdirect/esummary fixed version definition * resolved suggestion * updated main.nf * changed output definition * output: XML file * output definition: XML file * updated XML format in tests * updated test file * version: esummary instead of entrezdirect * output file pattern: *.esummary.xml * updated test file * updated versions * restored versions stdout * updated test file * changed xml_esummary pattern * changed entrezdirect to esummary version * updated test file * Update modules/entrezdirect/esummary/meta.yml changed output file pattern: "*.xml" Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/entrezdirect/esummary/meta.yml updated keywords Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/entrezdirect/esummary/main.nf Output file pattern: *.xml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/entrezdirect/esummary/main.nf Output file pattern: *.xml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/entrezdirect/esummary/main.nf database as separate input channel Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * removed blank spaces in input definition * database as separate channel * conditional script for stdin * updated input definition * entrez-direct version:16.2_1 * all input channels are separate * ignore stderr, catch xml stdout * removed blank lines * added ids file input * updated test * conditional script for input * removed bad definition of input file * updated test file * Update modules/entrezdirect/esummary/main.nf changed input definition: ui, uids_file Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/entrezdirect/esummary/meta.yml added uids_file description Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/entrezdirect/esummary/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * input: uid or uids_file * updated input * added uids_file to input * input file as optional input * input file as optional input in each test * new conditional script * unpdated test file * single input definition * added error messages * updated test * removed cat from command output * Update modules/entrezdirect/esummary/main.nf added comment on use of grep in output Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * added comment * removed blank spaces * input file: empty list * input file: empty list * removed comment at wrong position * optional file defined as empty list * updated successful test * Apply suggestions from code review Accepted suggestions. Co-authored-by: Matthieu Muffato <mm49@sanger.ac.uk> * Update modules/entrezdirect/esummary/main.nf Fixed comment. Co-authored-by: Matthieu Muffato <mm49@sanger.ac.uk> * Update modules/entrezdirect/esummary/main.nf Updated grep in output file. Co-authored-by: Matthieu Muffato <mm49@sanger.ac.uk> * added tail -n+3 before output * updated successful test Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> Co-authored-by: Matthieu Muffato <mm49@sanger.ac.uk>
26 lines
1.2 KiB
YAML
26 lines
1.2 KiB
YAML
- name: entrezdirect esummary test_entrezdirect_esummary_sra
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command: nextflow run ./tests/modules/entrezdirect/esummary -entry test_entrezdirect_esummary_sra -c ./tests/config/nextflow.config -c ./tests/modules/entrezdirect/esummary/nextflow.config
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tags:
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- entrezdirect
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- entrezdirect/esummary
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files:
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- path: output/entrezdirect/test_sra.xml
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md5sum: aeb7f5710a5447a8de89b9e6fc464606
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- name: entrezdirect esummary test_entrezdirect_esummary_genome
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command: nextflow run ./tests/modules/entrezdirect/esummary -entry test_entrezdirect_esummary_genome -c ./tests/config/nextflow.config -c ./tests/modules/entrezdirect/esummary/nextflow.config
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tags:
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- entrezdirect
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- entrezdirect/esummary
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files:
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- path: output/entrezdirect/test_genome.xml
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md5sum: 2abea497bcef9312105b23ed78b72f62
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- name: entrezdirect esummary test_entrezdirect_esummary_assembly
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command: nextflow run ./tests/modules/entrezdirect/esummary -entry test_entrezdirect_esummary_assembly -c ./tests/config/nextflow.config -c ./tests/modules/entrezdirect/esummary/nextflow.config
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tags:
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- entrezdirect
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- entrezdirect/esummary
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files:
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- path: output/entrezdirect/test_assembly.xml
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md5sum: b381959a000c1f3e8c18e7b35d7b2d0a
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