8 commits

Author	SHA1	Message	Date
Moritz E. Beber	f5baf910be	Apply suggestions from code review ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2022-04-03 00:21:09 +02:00
Moritz E. Beber	be93eae640	fix: insert .fastq file extension ... The MetaPhlAn3 module computes the input type from the file extension without the possibility to configure an override. Since AdapterRemoval2 creates files without `.fastq` extensions, MetaPhlAn3 input was determined to be SAM.	2022-04-02 21:50:13 +02:00
Moritz E. Beber	4eab257d68	style: prettify comment	2022-04-02 17:05:46 +02:00
James Fellows Yates	93aaa9eeac	Clean up AdapterRemoval and remove all debugging dumps	2022-04-01 21:36:22 +02:00
James A. Fellows Yates	03e832954f	Update subworkflows/local/shortread_adapterremoval.nf ... Co-authored-by: Moritz E. Beber <midnighter@posteo.net>	2022-04-01 20:55:33 +02:00
James A. Fellows Yates	14f2b7bd84	Apply suggestions from code review ... Co-authored-by: Moritz E. Beber <midnighter@posteo.net>	2022-04-01 15:34:05 +02:00
James Fellows Yates	dcda815bfb	Add final adapterremoval options to match fastp functionality	2022-04-01 09:50:08 +02:00
James Fellows Yates	c4c93bd59d	Start working on adding adapterremoval	2022-03-31 15:31:45 +02:00