3 commits

Author	SHA1	Message	Date
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	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