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5 commits

Author SHA1 Message Date
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
Matthieu Muffato
9deff5222e
Fixed the MD5 checksum (#1881) 2022-07-15 08:52:03 +02:00
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