Nomerge/first cwl files #135
Draft
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
mr-c
reviewed
May 3, 2023
Comment on lines
+44
to
+48
| - doc: "Please provide one sequence file with transcripts. Default: \"\". " | ||
| id: include | ||
| type: | ||
| - "null" | ||
| - string |
There was a problem hiding this comment.
I think this should be a File, yes?
Comment on lines
+51
to
+57
| - doc: "Please provide one *.genome file created with the genome command. Default: \"\". " | ||
| id: genome | ||
| type: | ||
| - "null" | ||
| - string | ||
| inputBinding: | ||
| prefix: --genome |
Comment on lines
+2
to
+8
| - doc: "Directory where input files can be found. Default: \"./\". " | ||
| id: in | ||
| type: | ||
| - "null" | ||
| - string | ||
| inputBinding: | ||
| prefix: --in |
There was a problem hiding this comment.
This will need overriding. Are there specific file extensions expected?
Comment on lines
+30
to
+36
| - doc: "Directory, where output files should be saved. Default: \"./\". " | ||
| id: out | ||
| type: | ||
| - "null" | ||
| - string | ||
| inputBinding: | ||
| prefix: --out |
There was a problem hiding this comment.
This option should be suppressed
Comment on lines
+30
to
+36
| - doc: "Directory, where output files should be saved. Default: \"./\". " | ||
| id: out | ||
| type: | ||
| - "null" | ||
| - string | ||
| inputBinding: | ||
| prefix: --out |
There was a problem hiding this comment.
This option should be suppressed
Comment on lines
+79
to
+85
| - doc: "Sequence file containing minimizers that should not be stored. Default: \"\". " | ||
| id: exclude | ||
| type: | ||
| - "null" | ||
| - string | ||
| inputBinding: | ||
| prefix: --exclude |
Comment on lines
+86
to
+92
| - doc: "Define which samples belong together, sum has to be equal to number of sequence files. Default: Every sequence file is one sample from one experiment. Default: []. " | ||
| id: samples | ||
| type: | ||
| - "null" | ||
| - boolean | ||
| inputBinding: | ||
| prefix: --samples |
Comment on lines
+100
to
+106
| - doc: "If set, names of the experiments are stored in a txt file. Default: 0. " | ||
| id: experiment-names | ||
| type: | ||
| - "null" | ||
| - boolean | ||
| inputBinding: | ||
| prefix: --experiment-names |
Comment on lines
+107
to
+113
| - doc: "Sequence file containing minimizers, only those minimizers will be considered for determining the expression thresholds. Default: \"\". " | ||
| id: levels-by-genome | ||
| type: | ||
| - "null" | ||
| - string | ||
| inputBinding: | ||
| prefix: --levels-by-genome |
Comment on lines
+2
to
+8
| - doc: "Directory, where output files should be saved. Default: \"./\". " | ||
| id: out | ||
| type: | ||
| - "null" | ||
| - string | ||
| inputBinding: | ||
| prefix: --out |
There was a problem hiding this comment.
This option should be suppressed
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.
First try of generated cwl files for needle