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Specify current Nextflow version to use in getting started docs Closes …
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…#250
@dweemx
dweemx committed Nov 12, 2020
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104 changes: 53 additions & 51 deletions docs/getting-started.rst
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@@ -22,6 +22,9 @@ Dependencies
Make sure you have the following software installed,

- Nextflow_

- Currently VSN-Pipelines requires Nextflow version ``20.04.1``

- A container system, either of:

- Docker_
@@ -61,59 +64,58 @@ Example Output

.. code:: shell
$ nextflow -C single_sample.config run vib-singlecell-nf/vsn-pipelines -entry single_sample
N E X T F L O W ~ version 19.12.0-edge
Launching `/ddn1/vol1/staging/leuven/stg_00002/lcb/dwmax/documents/aertslab/GitHub/vib-singlecell-nf/main.nf` [nice_engelbart] - revision: 0096df9054
$ nextflow -C nextflow.config run $VSN -entry single_sample
N E X T F L O W ~ version 20.04.1
Launching `/staging/leuven/stg_00002/lcb/dwmax/documents/aertslab/GitHub/vib-singlecell-nf/vsn-pipelines/main.nf` [silly_pare] - revision: 77be3ba59d
WARN: DSL 2 IS AN EXPERIMENTAL FEATURE UNDER DEVELOPMENT -- SYNTAX MAY CHANGE IN FUTURE RELEASE
executor > local (59)
[0c/d33a4e] process > single_sample:SINGLE_SAMPLE:UTILS__GENERATE_WORKFLOW_CONFIG_REPORT [100%] 1 of 1 ✔
[17/ab2b39] process > single_sample:SINGLE_SAMPLE:QC_FILTER:SC__FILE_CONVERTER (1) [100%] 2 of 2 ✔
[e4/84f688] process > single_sample:SINGLE_SAMPLE:QC_FILTER:SC__SCANPY__COMPUTE_QC_STATS (2) [100%] 2 of 2 ✔
[1b/daa1c3] process > single_sample:SINGLE_SAMPLE:QC_FILTER:SC__SCANPY__GENE_FILTER (2) [100%] 2 of 2 ✔
[fc/8653d0] process > single_sample:SINGLE_SAMPLE:QC_FILTER:SC__SCANPY__CELL_FILTER (2) [100%] 2 of 2 ✔
[9d/ebeff9] process > single_sample:SINGLE_SAMPLE:QC_FILTER:GENERATE_DUAL_INPUT_REPORT:SC__SCANPY__GENERATE_DUAL_INPUT_REPORT (2) [100%] 2 of 2 ✔
[87/e13dd0] process > single_sample:SINGLE_SAMPLE:QC_FILTER:GENERATE_DUAL_INPUT_REPORT:SC__SCANPY__REPORT_TO_HTML (2) [100%] 2 of 2 ✔
[a6/867a4a] process > single_sample:SINGLE_SAMPLE:NORMALIZE_TRANSFORM:SC__SCANPY__NORMALIZATION (2) [100%] 2 of 2 ✔
[07/8e63b1] process > single_sample:SINGLE_SAMPLE:NORMALIZE_TRANSFORM:SC__SCANPY__DATA_TRANSFORMATION (2) [100%] 2 of 2 ✔
[c1/07c18c] process > single_sample:SINGLE_SAMPLE:HVG_SELECTION:SC__SCANPY__FIND_HIGHLY_VARIABLE_GENES (2) [100%] 2 of 2 ✔
[e9/53e204] process > single_sample:SINGLE_SAMPLE:HVG_SELECTION:SC__SCANPY__SUBSET_HIGHLY_VARIABLE_GENES (2) [100%] 2 of 2 ✔
[0b/e7ae8c] process > single_sample:SINGLE_SAMPLE:HVG_SELECTION:SC__SCANPY__FEATURE_SCALING (2) [100%] 2 of 2 ✔
[5d/52236c] process > single_sample:SINGLE_SAMPLE:HVG_SELECTION:GENERATE_REPORT:SC__SCANPY__GENERATE_REPORT (2) [100%] 2 of 2 ✔
[71/5d6559] process > single_sample:SINGLE_SAMPLE:HVG_SELECTION:GENERATE_REPORT:SC__SCANPY__REPORT_TO_HTML (2) [100%] 2 of 2 ✔
[8c/1b4cc9] process > single_sample:SINGLE_SAMPLE:DIM_REDUCTION_PCA:SC__SCANPY__DIM_REDUCTION__PCA (2) [100%] 2 of 2 ✔
[7b/d423f7] process > single_sample:SINGLE_SAMPLE:NEIGHBORHOOD_GRAPH:SC__SCANPY__NEIGHBORHOOD_GRAPH (2) [100%] 2 of 2 ✔
[9b/3a10d2] process > single_sample:SINGLE_SAMPLE:DIM_REDUCTION_TSNE_UMAP:SC__SCANPY__DIM_REDUCTION__TSNE (2) [100%] 2 of 2 ✔
[5f/2c6325] process > single_sample:SINGLE_SAMPLE:DIM_REDUCTION_TSNE_UMAP:SC__SCANPY__DIM_REDUCTION__UMAP (2) [100%] 2 of 2 ✔
[ff/b5c6ef] process > single_sample:SINGLE_SAMPLE:DIM_REDUCTION_TSNE_UMAP:GENERATE_REPORT:SC__SCANPY__GENERATE_REPORT (2) [100%] 2 of 2 ✔
[b6/86bc36] process > single_sample:SINGLE_SAMPLE:DIM_REDUCTION_TSNE_UMAP:GENERATE_REPORT:SC__SCANPY__REPORT_TO_HTML (2) [100%] 2 of 2 ✔
[1a/2fec91] process > single_sample:SINGLE_SAMPLE:CLUSTER_IDENTIFICATION:SC__SCANPY__CLUSTERING (2) [100%] 2 of 2 ✔
[38/8a814b] process > single_sample:SINGLE_SAMPLE:CLUSTER_IDENTIFICATION:GENERATE_REPORT:SC__SCANPY__GENERATE_REPORT (2) [100%] 2 of 2 ✔
[35/530dcf] process > single_sample:SINGLE_SAMPLE:CLUSTER_IDENTIFICATION:GENERATE_REPORT:SC__SCANPY__REPORT_TO_HTML (2) [100%] 2 of 2 ✔
[05/3e201e] process > single_sample:SINGLE_SAMPLE:CLUSTER_IDENTIFICATION:SC__SCANPY__MARKER_GENES (2) [100%] 2 of 2 ✔
[04/ad44c6] process > single_sample:SINGLE_SAMPLE:SC__H5AD_TO_FILTERED_LOOM (2) [100%] 2 of 2 ✔
[46/47cac6] process > single_sample:SINGLE_SAMPLE:FILE_CONVERTER:SC__H5AD_TO_LOOM (2) [100%] 2 of 2 ✔
[33/640ffa] process > single_sample:SINGLE_SAMPLE:FILE_CONVERTER:COMPRESS_HDF5 (2) [100%] 2 of 2 ✔
[77/87b596] process > single_sample:SINGLE_SAMPLE:PUBLISH (2) [100%] 2 of 2 ✔
[61/82bf98] process > single_sample:SINGLE_SAMPLE:SC__SCANPY__MERGE_REPORTS (1) [100%] 2 of 2 ✔
[5a/26ce75] process > single_sample:SINGLE_SAMPLE:SC__SCANPY__REPORT_TO_HTML (2) [100%] 2 of 2 ✔
------------------------------------------------------------------
Converting 1k_pbmc_v2_chemistry.SC__SCANPY__MARKER_GENES.h5ad to 1k_pbmc_v2_chemistry.SC__SCANPY__MARKER_GENES.loom
(w/ additional compression)...
------------------------------------------------------------------
------------------------------------------------------------------
Converting 1k_pbmc_v3_chemistry.SC__SCANPY__MARKER_GENES.h5ad to 1k_pbmc_v3_chemistry.SC__SCANPY__MARKER_GENES.loom
(w/ additional compression)...
------------------------------------------------------------------
executor > local (83)
[44/e02c9e] process > single_sample:SINGLE_SAMPLE:SC__FILE_CONVERTER (1) [100%] 2 of 2 ✔
[22/723593] process > single_sample:SINGLE_SAMPLE:SCANPY__SINGLE_SAMPLE:QC_FILTER:SC__SCANPY__COMPUTE_QC_STATS (2) [100%] 2 of 2 ✔
[2e/10d845] process > single_sample:SINGLE_SAMPLE:SCANPY__SINGLE_SAMPLE:QC_FILTER:SC__SCANPY__CELL_FILTER (2) [100%] 2 of 2 ✔
[d6/fbe4b6] process > single_sample:SINGLE_SAMPLE:SCANPY__SINGLE_SAMPLE:QC_FILTER:SC__SCANPY__GENE_FILTER (2) [100%] 2 of 2 ✔
[22/d4a31b] process > single_sample:SINGLE_SAMPLE:SCANPY__SINGLE_SAMPLE:QC_FILTER:GENERATE_DUAL_INPUT_REPORT:SC__SCANPY__GENERATE_DUAL_INPUT_REPORT (2) [100%] 2 of 2 ✔
[20/b43313] process > single_sample:SINGLE_SAMPLE:SCANPY__SINGLE_SAMPLE:QC_FILTER:GENERATE_DUAL_INPUT_REPORT:SC__SCANPY__REPORT_TO_HTML (2) [100%] 2 of 2 ✔
[e3/ee3f9c] process > single_sample:SINGLE_SAMPLE:SCANPY__SINGLE_SAMPLE:NORMALIZE_TRANSFORM:SC__SCANPY__NORMALIZATION (2) [100%] 2 of 2 ✔
[79/7f4e25] process > single_sample:SINGLE_SAMPLE:SCANPY__SINGLE_SAMPLE:NORMALIZE_TRANSFORM:PUBLISH_H5AD_NORMALIZED:COMPRESS_HDF5 (2) [100%] 2 of 2 ✔
[40/370971] process > single_sample:SINGLE_SAMPLE:SCANPY__SINGLE_SAMPLE:NORMALIZE_TRANSFORM:PUBLISH_H5AD_NORMALIZED:SC__PUBLISH (2) [100%] 2 of 2 ✔
[f1/aa0726] process > single_sample:SINGLE_SAMPLE:SCANPY__SINGLE_SAMPLE:NORMALIZE_TRANSFORM:PUBLISH_H5AD_NORMALIZED:SC__PUBLISH_PROXY (2) [100%] 2 of 2 ✔
[76/e42ef9] process > single_sample:SINGLE_SAMPLE:SCANPY__SINGLE_SAMPLE:NORMALIZE_TRANSFORM:SC__SCANPY__DATA_TRANSFORMATION (2) [100%] 2 of 2 ✔
[04/11b8b8] process > single_sample:SINGLE_SAMPLE:SCANPY__SINGLE_SAMPLE:HVG_SELECTION:SC__SCANPY__FIND_HIGHLY_VARIABLE_GENES (2) [100%] 2 of 2 ✔
[1e/e1d058] process > single_sample:SINGLE_SAMPLE:SCANPY__SINGLE_SAMPLE:HVG_SELECTION:SC__SCANPY__SUBSET_HIGHLY_VARIABLE_GENES (2) [100%] 2 of 2 ✔
[07/b3580a] process > single_sample:SINGLE_SAMPLE:SCANPY__SINGLE_SAMPLE:HVG_SELECTION:SC__SCANPY__FEATURE_SCALING (2) [100%] 2 of 2 ✔
[b4/00bf5e] process > single_sample:SINGLE_SAMPLE:SCANPY__SINGLE_SAMPLE:HVG_SELECTION:PUBLISH_H5AD_HVG_SCALED:COMPRESS_HDF5 (2) [100%] 2 of 2 ✔
[8f/4d5d49] process > single_sample:SINGLE_SAMPLE:SCANPY__SINGLE_SAMPLE:HVG_SELECTION:PUBLISH_H5AD_HVG_SCALED:SC__PUBLISH (2) [100%] 2 of 2 ✔
[9a/3c5d0d] process > single_sample:SINGLE_SAMPLE:SCANPY__SINGLE_SAMPLE:HVG_SELECTION:PUBLISH_H5AD_HVG_SCALED:SC__PUBLISH_PROXY (2) [100%] 2 of 2 ✔
[dc/40cda6] process > single_sample:SINGLE_SAMPLE:SCANPY__SINGLE_SAMPLE:HVG_SELECTION:GENERATE_REPORT:SC__SCANPY__GENERATE_REPORT (2) [100%] 2 of 2 ✔
[62/9dc791] process > single_sample:SINGLE_SAMPLE:SCANPY__SINGLE_SAMPLE:HVG_SELECTION:GENERATE_REPORT:SC__SCANPY__REPORT_TO_HTML (2) [100%] 2 of 2 ✔
[8c/ed79b8] process > single_sample:SINGLE_SAMPLE:SCANPY__SINGLE_SAMPLE:DIM_REDUCTION_PCA:SC__SCANPY__DIM_REDUCTION__PCA (2) [100%] 2 of 2 ✔
[be/ed9c2e] process > single_sample:SINGLE_SAMPLE:SCANPY__SINGLE_SAMPLE:NEIGHBORHOOD_GRAPH:SC__SCANPY__NEIGHBORHOOD_GRAPH (2) [100%] 2 of 2 ✔
[01/ec367e] process > single_sample:SINGLE_SAMPLE:SCANPY__SINGLE_SAMPLE:DIM_REDUCTION_TSNE_UMAP:SC__SCANPY__DIM_REDUCTION__TSNE (2) [100%] 2 of 2 ✔
[ea/7fbf7c] process > single_sample:SINGLE_SAMPLE:SCANPY__SINGLE_SAMPLE:DIM_REDUCTION_TSNE_UMAP:SC__SCANPY__DIM_REDUCTION__UMAP (2) [100%] 2 of 2 ✔
[e5/a5a70a] process > single_sample:SINGLE_SAMPLE:SCANPY__SINGLE_SAMPLE:DIM_REDUCTION_TSNE_UMAP:GENERATE_REPORT:SC__SCANPY__GENERATE_REPORT (2) [100%] 2 of 2 ✔
[dd/b38b9b] process > single_sample:SINGLE_SAMPLE:SCANPY__SINGLE_SAMPLE:DIM_REDUCTION_TSNE_UMAP:GENERATE_REPORT:SC__SCANPY__REPORT_TO_HTML (2) [100%] 2 of 2 ✔
[5f/5bcb4d] process > single_sample:SINGLE_SAMPLE:SCANPY__SINGLE_SAMPLE:CLUSTER_IDENTIFICATION:SC__SCANPY__CLUSTERING (2) [100%] 2 of 2 ✔
[fa/9765a9] process > single_sample:SINGLE_SAMPLE:SCANPY__SINGLE_SAMPLE:CLUSTER_IDENTIFICATION:GENERATE_REPORT:SC__SCANPY__GENERATE_REPORT (2) [100%] 2 of 2 ✔
[aa/7b6adb] process > single_sample:SINGLE_SAMPLE:SCANPY__SINGLE_SAMPLE:CLUSTER_IDENTIFICATION:GENERATE_REPORT:SC__SCANPY__REPORT_TO_HTML (2) [100%] 2 of 2 ✔
[0f/82f171] process > single_sample:SINGLE_SAMPLE:SCANPY__SINGLE_SAMPLE:CLUSTER_IDENTIFICATION:SC__SCANPY__MARKER_GENES (2) [100%] 2 of 2 ✔
[96/04fc81] process > single_sample:SINGLE_SAMPLE:SCANPY__SINGLE_SAMPLE:UTILS__GENERATE_WORKFLOW_CONFIG_REPORT [100%] 1 of 1 ✔
[ee/7fe3fa] process > single_sample:SINGLE_SAMPLE:SCANPY__SINGLE_SAMPLE:SC__SCANPY__MERGE_REPORTS (2) [100%] 2 of 2 ✔
[6f/7cbcb5] process > single_sample:SINGLE_SAMPLE:SCANPY__SINGLE_SAMPLE:SC__SCANPY__REPORT_TO_HTML (2) [100%] 2 of 2 ✔
[87/7e681b] process > single_sample:SINGLE_SAMPLE:SCANPY__SINGLE_SAMPLE:FINALIZE:SC__H5AD_TO_FILTERED_LOOM (2) [100%] 2 of 2 ✔
[f0/176c0c] process > single_sample:SINGLE_SAMPLE:SCANPY__SINGLE_SAMPLE:FINALIZE:FILE_CONVERTER_TO_SCOPE:SC__H5AD_TO_LOOM (1) [100%] 2 of 2 ✔
[b3/608cde] process > single_sample:SINGLE_SAMPLE:SCANPY__SINGLE_SAMPLE:FINALIZE:FILE_CONVERTER_TO_SCANPY:SC__H5AD_MERGE (2) [100%] 2 of 2 ✔
[d1/43da78] process > single_sample:SINGLE_SAMPLE:SCANPY__SINGLE_SAMPLE:PUBLISH:SC__PUBLISH_PROXY (2) [100%] 2 of 2 ✔
[c3/6209f8] process > single_sample:PUBLISH_SINGLE_SAMPLE_SCOPE:COMPRESS_HDF5 (2) [100%] 2 of 2 ✔
[d5/e1a0c3] process > single_sample:PUBLISH_SINGLE_SAMPLE_SCOPE:SC__PUBLISH (2) [100%] 2 of 2 ✔
[4b/2e236a] process > single_sample:PUBLISH_SINGLE_SAMPLE_SCOPE:SC__PUBLISH_PROXY (2) [100%] 2 of 2 ✔
[87/f3f350] process > single_sample:PUBLISH_SINGLE_SAMPLE_SCANPY:COMPRESS_HDF5 (2) [100%] 2 of 2 ✔
[d4/2c09af] process > single_sample:PUBLISH_SINGLE_SAMPLE_SCANPY:SC__PUBLISH (2) [100%] 2 of 2 ✔
[da/3817b5] process > single_sample:PUBLISH_SINGLE_SAMPLE_SCANPY:SC__PUBLISH_PROXY (2) [100%] 2 of 2 ✔
WARN: To render the execution DAG in the required format it is required to install Graphviz -- See http://www.graphviz.org for more info.
Completed at: 25-Feb-2020 12:31:44
Duration : 2m 15s
CPU hours : 0.1
Succeeded : 59
Completed at: 12-Nov-2020 10:55:52
Duration : 2m 36s
CPU hours : 0.6
Succeeded : 83
The pipelines will generate 3 types of results in the output directory (`params.global.outdir`), by default ``out/``

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