Added new template, fixed mtbseq template #159
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
svarona
reviewed
Sep 27, 2023
svarona
reviewed
Sep 27, 2023
bu_isciii/templates/genomeev/DOC/viralrecon_sars_save_nohost.config
Outdated
Show resolved
Hide resolved
Shettland
reviewed
Sep 27, 2023
Shettland
reviewed
Sep 27, 2023
bu_isciii/templates/mtbseq_assembly/ANALYSIS/ANALYSIS02_MTBSEQ/lablog
Outdated
Show resolved
Hide resolved
Shettland
reviewed
Sep 27, 2023
bu_isciii/templates/mtbseq_assembly/ANALYSIS/ANALYSIS02_MTBSEQ/samples_all/lablog
Outdated
Show resolved
Hide resolved
Co-authored-by: Pablo Mata <[email protected]>
Shettland
reviewed
Sep 27, 2023
Comment on lines
1
to
3
| test_ref=$(cut -f2 samples_ref.txt | head -n1); if [ "$test_ref" == "NC_045512.2" ]; then rm create_summary_report_metagenomic.sh; mv create_summary_report_sars.sh create_summary_report.sh; else rm create_summary_report_sars.sh; mv create_summary_report_metagenomic.sh create_summary_report.sh; fi | ||
| test_ref=$(cut -f2 samples_ref.txt | head -n1); if [ "$test_ref" == "NC_045512.2" ]; then ANALYSIS_TYPE=AMPLICONS; else ANALYSIS_TYPE=METAGENOMIC; fi | ||
| test_ref=$(cut -f2 samples_ref.txt | head -n1); if [ "$test_ref" == "NC_045512.2" ]; then CONFIG_FILE=../../DOC/viralrecon_sars.config; else CONFIG_FILE="../../DOC/viralrecon_metagenomic.config"; fi |
There was a problem hiding this comment.
The sars config might be unnecessary for this pipeline, but im not sure.
There was a problem hiding this comment.
I was in the same situation so I kept it (you know, this is based on a previous service, and this is the script it used)
Co-authored-by: Pablo Mata <[email protected]>
Co-authored-by: Pablo Mata <[email protected]>
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.
MTBSeq template was a little bit suboptimal, I think its better now!
Besides, I added the genomeev template (I swear I was told to do it, if not we can delete it later)