added manifest information to the nextflow.config file to allow for remote execution
#204
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…e_typing multiple times.
remove manifest.config template adjusted tests for changes
Codecov Report
@@ Coverage Diff @@
## dev #204 +/- ##
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- Coverage 41.7% 41.64% -0.07%
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Files 71 71
Lines 6433 6426 -7
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- Hits 2683 2676 -7
Misses 3750 3750
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tiagofilipe12
approved these changes
Jun 11, 2019
| @@ -8,6 +8,10 @@ | |||
| - `Concoct`: Clustering metagenomic assembled comtigs with coverage and composition | |||
| - `MetaBAT2`: A robust statistical framework for reconstructing genomes from metagenomic data | |||
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| ### Minor/Other changes | |||
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| - added manifest information to the `nextflow.config` file to allow for remote execution | |||
bfrgoncalves
approved these changes
Jun 11, 2019
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Looks good! Just make sure to add a note at the PR description saying that this not solve all #194 issue but only one of the points.
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Thanks everyone for your comments! |
cimendes
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Jun 18, 2019
* remove submodule from dev install * fix typo * Added bwa component * Added cpus to bwa command * added manifest information to the `nextflow.config` file to allow for remote execution (#204) - Partial solve to #194 issue - Deprecation of the `manifest.config´ file - Add the manifest information to the `nextflow.config` file * Added component for haplotypecaller * Added merge vcfs to haplotypecaller component * Added mark duplicates component * Added bam index to mark duplicates * Added base_recalibrator component * Removed publishDir for haplotypecaller * Added apply_bqsr process to base_recalibrator component * Updated changelog * Added description to haplotypecaller * Add check for the location of specific dot files * Updated changelog * Updated version
cimendes
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Jul 4, 2019
cimendes
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Sep 16, 2019
* Dag files (#209) * move DAG JSON files to the resources directory * added manifest information to the `nextflow.config` file to allow for remote execution (#204) - Partial solve to #194 issue - Deprecation of the `manifest.config´ file * Set phred encoding when it fails to be determined - trimmomatic (#211) * fix bug publishdir (downsample_fastq component) * add pphred33 when encoding fails to be determined, if still fails retry with phred64 encoding (trimmomatic component) * Fix downsample (#222) * edited file names for downsample fastqs * stringified depth for file name
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This is a solution for resolving the issue reported at #194
The manifest.config file has been deprecated and instead it's information (main and nameScript) are now included in nextflow.config file.