James A. Fellows Yates
90aef30f43
Set process label to process_single for modules with no task.cpus usage ( #2076 )
...
* Set process label to `process_single` for modules with no `task.cpus` usage
* Fix tests of 'borked' modules
* prettier
* More modules are single-threaded and can use process_single
* Adding process_single to hmmer/esl* modules
* Fix failing tests
* Prettier
Co-authored-by: Matthieu Muffato <mm49@sanger.ac.uk>
Co-authored-by: Daniel Lundin <erik.rikard.daniel@gmail.com>
2022-09-19 11:54:47 +02:00
Alexander Ramos Díaz
4ed5dc4593
new (fixed) module: entrezdirect/esearch ( #1927 )
...
* added module files
* latest version
* latest version
* latest version
* latest version
* updated test, failing
* added comment on why to use tail -n+3
* same as latest test
* moved args to the end of script
* updated test
* double quotes for esearch input
* removed tail -n+3, stderr is redirected by nextflow
* changed single to double quotes
* Update modules/entrezdirect/esearch/main.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/entrezdirect/esearch/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update meta.yml
removed default from database parameter
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-07-26 09:07:38 -06:00
Alexander Ramos Díaz
ad426cb18c
new (fixed) module: entrezdirect/xtract ( #1926 )
...
* first commit: module files
* last version main.nf
* modules/entrezdirect/xtract/meta.yml
* updated file
* updated test
* Update modules/entrezdirect/xtract/main.nf
changed name of output file
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/entrezdirect/xtract/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update tests/modules/entrezdirect/xtract/main.nf
Co-authored-by: Matthieu Muffato <mm49@sanger.ac.uk>
* Update tests/modules/entrezdirect/xtract/main.nf
Co-authored-by: Matthieu Muffato <mm49@sanger.ac.uk>
* updated test, removed esummary input file
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: Matthieu Muffato <mm49@sanger.ac.uk>
2022-07-26 08:58:49 -06:00
Alexander Ramos Díaz
f420d97ca2
renamed output in entrezdirect/esummary: xml ( #1928 )
...
* renamed output: xml
* removed tail -n+3 from output
* removed comment
* removed blank space
* removed blank space
* updated test
2022-07-26 08:33:02 -06:00
Alexander Ramos Díaz
b4452a4881
Add ENTREZDIRECT/ESUMMARY ( #1833 )
...
* 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>
2022-07-13 11:26:58 -06:00
