[nf-core] Questions about rMATS parameters

[Uri David Akavia]

Hi

I'm trying to implement rMATS in nf-core, see https://github.com/nf-core/modules/issues/8699, and in this version of nf-core, you have to separate optional and obligatory parameters.

I'm planning to have a module for prep, post (which will be run without stats) and stats.

I have some questions about parmeters, and I'm not sure which parameter belongs to each task. So I've listed them down as I understand them.

Please let me know if I've gotten them wrong.

Thank you very much!

Uri David

Prep obligatory parameters

======================

--gtf GTF

--b1 (or --s1)

 --od OD               The directory for final output from the post step
  --tmp TMP             

 --readLength READLENGTH

Prep optional parameters

====================

 --variable-read-length
  --anchorLength ANCHORLENGTH

-t paired/single

--libType {fr-unstranded,fr-firststrand,fr-secondstrand}

--tophatAnchor

--bi BINDEX

--nthread

--novelSS

--mil

--mel

--allow-clipping

Post obligatory parameters

=====================

--gtf GTF

--b1 (or --s1)

 --od OD               The directory for final output from the post step
  --tmp TMP             

 --readLength READLENGTH

--statoff (if I don't want stats, just post)

Post optional parameters 

====================

 --variable-read-length
  --anchorLength ANCHORLENGTH

-t paired/single

--libType {fr-unstranded,fr-firststrand,fr-secondstrand}

--nthread

--individual-counts

Stat obligatory parameters

======================

--gtf GTF

--b1 (or --s1)

 --od OD               The directory for final output from the post step
  --tmp TMP             

 --readLength READLENGTH

Stat optional parameters

====================

--cstat

--paired-stats

--darts-model

--darts-cutoff

--individual-counts

[kutsc...@gmail.com]

The parameter details you posted are mostly correct

For the prep step, --bi BINDEX is required if using --s1

For the post and stat steps, --b1 is required. If --s1 was used in the prep step then it would have created bam files and those file names will need to be used as --b1 in the post and stat steps https://github.com/Xinglab/rmats-turbo/issues/208

For the stat step, two groups are required. Either the output from a post step that used both --b1 and --b2 is needed or the output can be split into two groups like: https://github.com/Xinglab/rmats-turbo/tree/v4.3.0?tab=readme-ov-file#running-the-statistical-model-separately

Here's which parameters are required/optional for each step

--gtf GTF: required for prep and post
--b1 B1, --b2 B2, --s1 S1, --s2 S2: The prep step requires at least one. The post step requires --b1, or --b2, or both
--od OD and --tmp TMP: always required
-t: has a default value. Used in the prep step
--libType: has a default value. Used in the prep step
--readLength READLENGTH: required for prep and post
--variable-read-length: optional and only used in the prep step
--anchorLength ANCHORLENGTH: has a default value. Used in prep and post
--tophatAnchor TOPHATANCHOR: has a default value: Only used in the prep step with --s1 or --s2
--bi BINDEX: required if --s1 or --s2 is used
--nthread NTHREAD: has a default value. Used in prep, post, and stat
--tstat TSTAT: has a default value. Used in stat
--cstat CSTAT: has a default value. Used in stat
--statoff: optional and only used in the post step
--paired-stats: optional and only used in the stat step
--darts-model: optional and only used in the stat step
--darts-cutoff: has a default value. Only used in the stat step if --darts-model
--novelSS: optional and only used in prep and post
--mil MIL: has a default value. Only used in prep and post
--mel MEL: has a default value. Only used in prep and post
--allow-clipping: optional and only used in the prep step
--fixed-event-set FIXED_EVENT_SET: optional and only used in the post step
--individual-counts: optional and only used in the post step

Eric