[med-svn] [Git][med-team/pigx-scrnaseq][master] Series of patches addressing test failures
Steffen Möller
gitlab at salsa.debian.org
Sat Sep 12 02:06:24 BST 2020
Steffen Möller pushed to branch master at Debian Med / pigx-scrnaseq
Commits:
153e5eee by Steffen Möller at 2020-09-12T03:05:51+02:00
Series of patches addressing test failures
- - - - -
9 changed files:
- debian/control
- + debian/patches/BAMTagHistogram2BamTagHistogram.patch
- + debian/patches/DataFrameDeprecation.patch
- + debian/patches/FilterBAM2FilterBam.patch
- + debian/patches/ReduceJobsDuringTesting.patch
- + debian/patches/TagReadWithGeneExon2TagReadWithGeneExonFunction.patch
- + debian/patches/series
- + debian/patches/tmp_testing_survival.patch
- debian/rules
Changes:
=====================================
debian/control
=====================================
@@ -9,7 +9,33 @@ Build-Depends: debhelper (>= 11),
python3-loompy,
python3-pandas,
python3-magic,
- r-cran-dplyr
+ r-cran-dplyr,
+ r-other-rajewsky-dropbead,
+ r-cran-rmarkdown,
+ r-bioc-scater,
+ r-bioc-scran,
+ snakemake,
+ rna-star,
+ fastqc,
+ samtools,
+ pandoc,
+ r-bioc-genomicalignments,
+ r-bioc-genomicfiles,
+ r-bioc-genomicranges,
+ r-cran-ggplot2,
+ r-bioc-rsamtools,
+ r-bioc-delayedmatrixstats,
+ r-bioc-delayedarray,
+ r-bioc-singlecellexperiment,
+ r-cran-dt,
+ r-bioc-hdf5array,
+ r-cran-rtsne,
+ r-cran-data.table,
+ r-cran-cowplot,
+ r-cran-stringr,
+ r-cran-yaml,
+ r-cran-pheatmap,
+ r-bioc-rtracklayer,
Standards-Version: 4.5.0
Homepage: https://github.com/BIMSBbioinfo/pigx_scrnaseq
Vcs-Browser: https://salsa.debian.org/med-team/pigx-scrnaseq
=====================================
debian/patches/BAMTagHistogram2BamTagHistogram.patch
=====================================
@@ -0,0 +1,31 @@
+Index: pigx-scrnaseq/Snake_Dropseq.py
+===================================================================
+--- pigx-scrnaseq.orig/Snake_Dropseq.py
++++ pigx-scrnaseq/Snake_Dropseq.py
+@@ -146,7 +146,7 @@ MAP_scRNA = expand(os.path.join(PATH_MAP
+
+ # ----------------------------------------------------------------------------- #
+ # Number of reads per cell calculation
+-BAM_HISTOGRAM = expand(os.path.join(PATH_MAPPED, "{name}", "{genome}",'{name}_{genome}_BAMTagHistogram.txt'), genome = REFERENCE_NAMES, name = SAMPLE_NAMES)
++BAM_HISTOGRAM = expand(os.path.join(PATH_MAPPED, "{name}", "{genome}",'{name}_{genome}_BamTagHistogram.txt'), genome = REFERENCE_NAMES, name = SAMPLE_NAMES)
+
+ # ----------------------------------------------------------------------------- #
+ # Number of reads per cell calculation
+@@ -834,7 +834,7 @@ rule bam_tag_histogram:
+ input:
+ infile = rules.tag_with_gene_exon.output.outfile
+ output:
+- outfile = os.path.join(PATH_MAPPED, "{name}", "{genome}",'{name}_{genome}_BAMTagHistogram.txt')
++ outfile = os.path.join(PATH_MAPPED, "{name}", "{genome}",'{name}_{genome}_BamTagHistogram.txt')
+ params:
+ outdir = os.path.join(PATH_MAPPED, "{name}", "{genome}"),
+ outname = "{name}_{genome}",
+@@ -843,7 +843,7 @@ rule bam_tag_histogram:
+ java = SOFTWARE['java']['executable'],
+ droptools = SOFTWARE['droptools']['executable'],
+ tempdir = TEMPDIR,
+- app_name = 'BAMTagHistogram'
++ app_name = 'BamTagHistogram'
+ message: """
+ BamTagHistogram:
+ input: {input.infile}
=====================================
debian/patches/DataFrameDeprecation.patch
=====================================
@@ -0,0 +1,21 @@
+Index: pigx-scrnaseq/scripts/convert_matrix_to_loom.py
+===================================================================
+--- pigx-scrnaseq.orig/scripts/convert_matrix_to_loom.py
++++ pigx-scrnaseq/scripts/convert_matrix_to_loom.py
+@@ -20,7 +20,8 @@ def get_all_gene_ids (gtf_file):
+ # parse the gene x cell matrix file and return a matrix object, row attributes along with column attributes (necessary to construct a loom file)
+ def parse_umi_matrix_file (matrix_file):
+ df = pandas.read_table(input_file, index_col=0)
+- matrix = pandas.DataFrame.as_matrix(df)
++ #matrix = pandas.DataFrame.as_matrix(df)
++ matrix = df.values
+ row_names = list(df.index)
+ col_names = list(df.columns)
+ return(matrix, row_names, col_names)
+@@ -63,4 +64,4 @@ if __name__ == '__main__':
+ col_attrs = { "cell_id": ['_'.join([sample_id, cn]) for cn in col_names] } #prepend sample ids to the cell ids
+ loompy.create(output_filepath, umi_matrix, row_attrs, col_attrs)
+
+-
+\ No newline at end of file
++
=====================================
debian/patches/FilterBAM2FilterBam.patch
=====================================
@@ -0,0 +1,13 @@
+Index: pigx-scrnaseq/Snake_Dropseq.py
+===================================================================
+--- pigx-scrnaseq.orig/Snake_Dropseq.py
++++ pigx-scrnaseq/Snake_Dropseq.py
+@@ -581,7 +581,7 @@ rule filter_bam:
+ params:
+ droptools = SOFTWARE['droptools']['executable'],
+ java = SOFTWARE['java']['executable'],
+- app_name = 'FilterBAM',
++ app_name = 'FilterBam',
+ threads = config['execution']['rules']['filter_bam']['threads'],
+ mem = config['execution']['rules']['filter_bam']['memory'],
+ tempdir = TEMPDIR
=====================================
debian/patches/ReduceJobsDuringTesting.patch
=====================================
@@ -0,0 +1,13 @@
+Index: pigx-scrnaseq/tests/settings_cluster.yaml
+===================================================================
+--- pigx-scrnaseq.orig/tests/settings_cluster.yaml
++++ pigx-scrnaseq/tests/settings_cluster.yaml
+@@ -16,7 +16,7 @@ execution:
+
+ execution:
+ submit-to-cluster: yes
+- jobs: 6
++ jobs: 1
+ nice: 19
+ cluster:
+ missing-file-timeout: 120
=====================================
debian/patches/TagReadWithGeneExon2TagReadWithGeneExonFunction.patch
=====================================
@@ -0,0 +1,13 @@
+Index: pigx-scrnaseq/Snake_Dropseq.py
+===================================================================
+--- pigx-scrnaseq.orig/Snake_Dropseq.py
++++ pigx-scrnaseq/Snake_Dropseq.py
+@@ -783,7 +783,7 @@ rule tag_with_gene_exon:
+ params:
+ droptools = SOFTWARE['droptools']['executable'],
+ java = SOFTWARE['java']['executable'],
+- app_name = 'TagReadWithGeneExon',
++ app_name = 'TagReadWithGeneExonFunction',
+ threads = config['execution']['rules']['tag_with_gene_exon']['threads'],
+ mem = config['execution']['rules']['tag_with_gene_exon']['memory'],
+ tempdir = TEMPDIR
=====================================
debian/patches/series
=====================================
@@ -0,0 +1,6 @@
+FilterBAM2FilterBam.patch
+ReduceJobsDuringTesting.patch
+tmp_testing_survival.patch
+TagReadWithGeneExon2TagReadWithGeneExonFunction.patch
+BAMTagHistogram2BamTagHistogram.patch
+DataFrameDeprecation.patch
=====================================
debian/patches/tmp_testing_survival.patch
=====================================
@@ -0,0 +1,13 @@
+Index: pigx-scrnaseq/Snake_Dropseq.py
+===================================================================
+--- pigx-scrnaseq.orig/Snake_Dropseq.py
++++ pigx-scrnaseq/Snake_Dropseq.py
+@@ -285,7 +285,7 @@ rule make_star_reference:
+ gtf : {input.gtf}
+ """
+ shell:"""
+- {params.star} {params.star_args} --runMode genomeGenerate --genomeDir {params.outdir} --genomeFastaFiles {input.fasta} --runThreadN {params.threads} --sjdbGTFfile {input.gtf} --sjdbOverhang 99
++ {params.star} {params.star_args} --runMode genomeGenerate --genomeDir {params.outdir} --genomeFastaFiles {input.fasta} --runThreadN {params.threads} --sjdbGTFfile {input.gtf} --sjdbOverhang 99 --genomeSAindexNbases 10
+ touch {output.outfile} 2> {log}
+ """
+
=====================================
debian/rules
=====================================
@@ -10,3 +10,6 @@ export DROPSEQJAR=/usr/share/java/dropseq.jar
override_dh_auto_clean:
dh_auto_clean
rm -f config.log
+ rm -f tests/out/FASTQC/HEK_0h_br1_R2_1_fastqc.zip tests/out/FASTQC/HEK_0h_br1_R2_2.fastq.gz.fastqc.done tests/out/FASTQC/HEK_0h_br1_R2_2_fastqc.zip tests/out/Log/hg19.make_star_reference.log
+ rm -f tests/out/pigx_work/bin/Rscript tests/out/pigx_work/bin/pandoc tests/out/pigx_work/bin/pandoc-citeproc tests/out/Annotation/hg19/hg19.fasta tests/out/Annotation/hg19/hg19.gtf
+ rm -rf tests/out
View it on GitLab: https://salsa.debian.org/med-team/pigx-scrnaseq/-/commit/153e5eeebcc6bb59e7a6dfcbd3a8e5d2ced388ec
--
View it on GitLab: https://salsa.debian.org/med-team/pigx-scrnaseq/-/commit/153e5eeebcc6bb59e7a6dfcbd3a8e5d2ced388ec
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