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Develop for v0.22.0 #262
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Develop for v0.22.0 #262
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…names and add comments to pipelines in main.nf to detail precisely I/O of the pipelines. This regards:
- single_sample_decontx_scrublet
- single_sample_soupx
- single_sample_soupx_scrublet
…amination with the filterEmptyCells parameter
…he data. Let this be handled by the parent workflows. This option is better especially when when don't what to perform the basic filtering but want to annotate the data.
…Let this be handled by the parent workflows. This option is better especially when when don't what to perform the basic filtering but want to annotate the data.
- Add plots for the n_counts filter in filter QC report python notebook - Closes vib-singlecell-nf/scanpy#47
…sources__cpu label
…if n_jobs is > 1)
… that directs output will be included in final loom.
…operator which won't work if array have different lengths
Plus use safe navigation operator in single_sample nxf workflow
…e for the harmony pipelines
…elWithIndex when calling it multiple times (e.g.: main_atac.nf, atac_qc_filtering). This due to the scope badly definef for some variables inside the loop of extractSample
…elWithIndex when calling it multiple times (e.g.: main_atac.nf, atac_qc_filtering). This due to the scope badly definef for some variables inside the loop of extractSample [part 2]
- Remove popscle.nf from main repo workflows. The freemuxlet/demuxlet workflows in the popscle repo are now called directly. - Change freemuxlet/demuxlet references in main.nf to point to the popscle repor workflows, and to use the cellranger_dataChannel_to_bam_barcodes function to format the input data channel.
- Include fix to properly resolve files from the cellranger path
- Update to pySCENIC 0.10.4 - GRN output with correlations is now published to the scenic output location - Fixes #254
…_grn_cor Feature/254 Add TF-gene correlations to the SCENIC GRN output
…opscle_inputs Feature/255 reformat popscle inputs
KrisDavie
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Develop for v0.22.0 Former-commit-id: bf6f7c4
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Summary of changes:
839735e a463b8a Pre-filtering/pre-annotating (FILTER_AND_ANNOTATE_AND_CLEAN) is now performed outside of QC_FILTER
c32cfce Add sanity check - Check if column containing sample ID exists in metadata file
47e611e *scrublet workflows - Publish data with doublets removed
822fc95 Support to tag final output files (loom, h5ad) with the batch variabe for the harmony pipelines
Merge pull request Feature/255 reformat popscle inputs #256 - Reformat popscle inputs Closes [SUGGESTION] Freemuxlet and demuxlet should be able run on any bam and barcodes input #255
22d587c Bug fix - Pipeline should output scopeloom instead of FINALIZE.out.scopeloom so that directs output will be included in final loom.
f50074a d0eb654 Bug fix - Fix bug leading to out of sync issues of the input params of getChannel when calling it multiple times
2b1bd4e Bug fix - Closes [BUG] AttributeError: 'numpy.ndarray' object has no attribute 'nnz' #260
923baad Specify current Nextflow version to use in getting started docs Closes [BUG]Module compile error #250
099b2f0 Bug fix - Fix bug when plotting density plot when no outliers found.
648b4df Add support to remove empty cells after DecontX matrix decontamination with the filterEmptyCells parameter
b1923bb Add plots for the n_counts filter in filter QC report python notebook and Closes Add strategy filter based on adaptive thresholds (e.g.: MAD) scanpy#47
4915786 Add single_sample_qc workflow
23520e0 Set the n_jobs argument in regress out step using compute_resources__cpu label
262c219 Disable BLAS multithreading in regress out step to reduce cpu usage (especially if n_jobs is > 1)
debb6a1 Add clustering preflight checks Closes [SUGGESTION] Scanpy find markers step can fail when only one cluster found from clustering algorithm scanpy#48
26e57f2 Bug fix - Fix bug belong to scanpy not sc in config
d723bdd Bug fix - Use np.array_equel for array comparison instead of equality operator which won't work if array have different lengths
2d9fa8f Disable multi-threading for cisTarget and AUCell step to reduce cpu usage
Merge pull request Feature/254 Add TF-gene correlations to the SCENIC GRN output #257 - Add TF-gene correlations to the SCENIC GRN output Closes Adding correlation to GRNBoost adjency table #254
b543a8b Closes Fails when toNPCs param is higher than the feature dimension pcacv#14
ef7ab83 Closes Non integer strings are not accepted by R pcacv#8
b04d121 Closes Add a fallback on the number of PCs returned if no optimum found pcacv#15
228276f Adapt *-n-pc and k parameters if violating requirement of data dimensionality
4d12b74 - Bug fix - Fix config: missing assignment operator