Merge branch 'develop'

ddesvillechabrol · Aug 29, 2017 · 803f139 · 803f139
2 parents 8c6652e 825ff52
commit 803f139
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Showing 6 changed files with 11 additions and 10 deletions.
diff --git a/sequana/pipelines/atac-seq/config.yaml b/sequana/pipelines/atac-seq/config.yaml
@@ -54,7 54,7 @@ bowtie2_mapping:
 
 mark_duplicates:
  remove: 'True' ## may be False
- tmpdir: 'TMP_DIR=/local/scratch/' ## on Slurm cluster at Pasteur
  tmpdir: 'TMP_DIR=/local/scratch/' # Path to the temporary directory on your cluster, may be "TMP_DIR=/tmp" also
 
 ##################################################################
 # PEAK CALLING SECTION

diff --git a/sequana/pipelines/rnaseq/config.yaml b/sequana/pipelines/rnaseq/config.yaml
@@ -170,7 170,7 @@ bowtie1_mapping_rna:
 #
 star_mapping:
  do: no
- options: ""
  options: "--outFilterMismatchNoverLmax 0.05 --outSAMunmapped Within "
  threads: 4
 
 #############################################################################
@@ -282,8 282,9 @@ coverage:
 #
 mark_duplicates:
  do: no
- remove: 'True' ## may be False
- tmpdir: "TMP_DIR=/local/scratch/" ## on Slurm cluster at Pasteur
  remove: 'False' ## may be False
  tmpdir: "TMP_DIR=/local/scratch/" # Path to the temporary directory on your cluster, may be "TMP_DIR=/tmp" also
  threads: 4
 
 
 #############################################################################

diff --git a/sequana/rules/Adapters/cutadapt/cutadapt.rules b/sequana/rules/Adapters/cutadapt/cutadapt.rules
@@ -63,6 63,8 @@ rule cutadapt:
 
  if config['cutadapt']['design_file']:
  from sequana import FindAdaptersFromDesign
  # FIXME how important is this that the sample name contains a _
  # character ?
  sample = params.sample.split("_")[0]
  fa = FindAdaptersFromDesign(params.design, params.design_adapter)
  fwd, rev = fa.save_adapters_to_fasta(sample, output_dir=params.wkdir)

diff --git a/sequana/rules/Mapping/star_mapping/star_mapping.rules b/sequana/rules/Mapping/star_mapping/star_mapping.rules
@@ -50,8 50,6 @@ rule star_mapping:
  --readFilesIn {input.fastq} \
  --runThreadN {threads} \
  --genomeLoad NoSharedMemory \
- --outFilterMismatchNoverLmax 0.05 \
- --outSAMunmapped Within \
  --outSAMtype BAM SortedByCoordinate \
  --readFilesCommand zcat \
  --seedSearchStartLmax 20 \
@@ -76,8 74,6 @@ rule star_mapping:
  --runThreadN {threads} \
  --genomeLoad NoSharedMemory \
  --sjdbFileChrStartEnd {params.splice_file} \
- --outFilterMismatchNoverLmax 0.05 \
- --outSAMunmapped Within \
  --outSAMtype BAM SortedByCoordinate \
  --readFilesCommand zcat \
  --outFileNamePrefix {params.prefix2} \

diff --git a/sequana/rules/picard-tools/mark_duplicates/mark_duplicates.rules b/sequana/rules/picard-tools/mark_duplicates/mark_duplicates.rules
@@ -26,6 26,8 @@ rule mark_duplicates:
  params:
  remove = config["mark_duplicates"]["remove"],
  tmpdir = config["mark_duplicates"]["tmpdir"]
  threads:
  int(config["mark_duplicate"]["threads"])
  shell:
  """
  (picard MarkDuplicates I={input} O={output.bam} \

diff --git a/setup.py b/setup.py
@@ -7,8 7,8 @@
 import glob
 
 _MAJOR = 0
-_MINOR = 4
-_MICRO = 2
 _MINOR = 5
 _MICRO = 0
 version = '%d.%d.%d' % (_MAJOR, _MINOR, _MICRO)
 release = '%d.%d' % (_MAJOR, _MINOR)