Fix caching problems #83
Merged
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Merged
rreggiar
approved these changes
Nov 27, 2023
| @@ -1,3 +1,5 @@ | |||
| #!/usr/bin/env python | |||
There was a problem hiding this comment.
not for this PR, but in general can you add author and license please to your custom scripts?
There was a problem hiding this comment.
This script contains the requested information in lines 7-10. Maybe not in the expected location, but the only thing I did here was adding the shebang. Quickly went through all the other scripts, found author and license in various formats in all of them.
Should I unify the formatting of this information across all files?
modules/local/fasta/main.nf
Outdated
Comment on lines
11
to
13
| tuple val(meta), path(bed, name: "bed.input") | ||
| path fasta, name: "fasta.input" | ||
|
|
There was a problem hiding this comment.
why are you naming the input here?
There was a problem hiding this comment.
I think this should better be handled using task.ext.prefix in the modules.config - will quickly do that
There was a problem hiding this comment.
Ok there was not even a file name collission, don't know why I did that
There was a problem hiding this comment.
Okay I found the reason for this now: There are parts of this process which manipulate all files that end with *.fa and *.fasta. If the input has one of this extensions, it will not work properly. I temporarily re-activated this, since restructuring of the process is not in the scope of this PR but I will handle this soon.
|
nictru
force-pushed
the
caching
branch
2 times, most recently
from
e15a961 to
eecedfd
Compare
MariekeVromman
approved these changes
Jan 30, 2024
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
This PR fixes some general pipeline problems: