-
Notifications
You must be signed in to change notification settings - Fork 0
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
Input can be a path prefix #24
Merged
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
nh13
changed the base branch from
main
to
feature/sample-sheet-output-to-project
November 15, 2022 06:49
nh13
commented
Nov 15, 2022
nh13
force-pushed
the
feature/sample-sheet-output-to-project
branch
from
November 15, 2022 18:50
5fc25d3
to
c36929a
Compare
nh13
force-pushed
the
feature/path-prefix-as-input-infer-kind
branch
from
November 15, 2022 18:52
d5d9495
to
639692c
Compare
Base automatically changed from
feature/sample-sheet-output-to-project
to
main
November 15, 2022 18:57
tfenne
suggested changes
Nov 15, 2022
tfenne
approved these changes
Nov 17, 2022
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
A few minor comments and suggestions, but good to merge once you're happy.
Co-authored-by: Tim Fennell <tfenne@tfenne.com>
Co-authored-by: Tim Fennell <tfenne@tfenne.com>
nh13
force-pushed
the
feature/path-prefix-as-input-infer-kind
branch
from
November 17, 2022 16:22
372ca33
to
7542c8d
Compare
omicsorama
approved these changes
Nov 23, 2022
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Outdated suggestions cannot be applied.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.
The user may provide a path prefix (or directory) in which undetermined FASTQs live. The file names are assumed to be of the form:
<*>_L00#_<R# or I#>_001.fastq.gz
. The following can be inferred from this pattern: the lane number, read number, and if the FASTQ is a template or index read.If no read structure is given either on the command line or Sample Sheet, then a new list of read structure is built, one per input FASTQ, where the kind (segment type) is inferred from the file name and all bases are used. E.g.
would yield the read structures
+B +T +T +B
. Reads will all molecular barcodes are supported (e.g.test_L001_U1.fastq.gz
) and bases to skip (e.g.test_L001_S1.fastq.gz
). The utility of the latter is questionable, but kept for completeness.Improvement: due to the need for all sample barcode read segments to have a fixed length (for index hopping metrics collection and some validation), the first read is read from each FASTQ that contains a variable length sample barcode to determine the read length and fix the length of the variable length sample barcode. I don't believe that a read structure like
+B +T +T +B
previously worked!