From 97706eadae0ae150707360be88fcd7792d4206cc Mon Sep 17 00:00:00 2001 From: LeilyR Date: Fri, 24 Apr 2020 18:20:21 +0200 Subject: [PATCH] Develop (#625) * fixed a typo in alignment sieve rule (#623) Please enter the commit message for your changes. Lines starting Co-authored-by: Leily Rabbani * Atac log (#624) * fixed a typo in alignment sieve rule Please enter the commit message for your changes. Lines starting * ncreased the version Co-authored-by: Leily Rabbani Co-authored-by: Leily Rabbani --- conda-recipe/meta.yaml | 2 +- docs/content/News.rst | 9 ++++++--- snakePipes/__init__.py | 2 +- snakePipes/shared/rules/ATAC.snakefile | 6 +++--- 4 files changed, 11 insertions(+), 8 deletions(-) mode change 100644 => 100755 conda-recipe/meta.yaml mode change 100644 => 100755 docs/content/News.rst mode change 100644 => 100755 snakePipes/__init__.py mode change 100644 => 100755 snakePipes/shared/rules/ATAC.snakefile diff --git a/conda-recipe/meta.yaml b/conda-recipe/meta.yaml old mode 100644 new mode 100755 index 51d706b42..a05ca5296 --- a/conda-recipe/meta.yaml +++ b/conda-recipe/meta.yaml @@ -1,6 +1,6 @@ package: name: snakepipes - version: 2.1.0 + version: 2.1.1 source: path: ../ diff --git a/docs/content/News.rst b/docs/content/News.rst old mode 100644 new mode 100755 index 02187c842..70ff3e076 --- a/docs/content/News.rst +++ b/docs/content/News.rst @@ -1,5 +1,8 @@ snakePipes News =============== +snakePipes 2.1.1 +---------------- +* small bug fix: a typo in atac-seq pipeline snakePipes 2.1.0 ---------------- @@ -90,14 +93,14 @@ snakePipes 1.2.3 * Fixed CSAW QC plot error with single end reads * Updated histone HMM environment to a working conda version * Salmon_wasabi is now a localrule - + snakePipes 1.2.2 ---------------- * Fixed a bug in the ATAC-seq environment where GenomeInfoDbData was missing. * Also an occasional issue with CSAW - + snakePipes 1.2.1 ---------------- @@ -106,7 +109,7 @@ snakePipes 1.2.1 * Implemented complex experimental design in RNAseq (differential gene expression), ChIP/ATACseq (differential binding). * Fixed an issue with ggplot2 and log transformation in RNAseq report Rmd. * fastqc folder is created and its content will be added to multiqc only if fastqc flag is called. - * fastqc-trimmed folder is created and its content will be added to multiqc only if both fastqc and trim flags are called. + * fastqc-trimmed folder is created and its content will be added to multiqc only if both fastqc and trim flags are called. snakePipes 1.2.0 ---------------- diff --git a/snakePipes/__init__.py b/snakePipes/__init__.py old mode 100644 new mode 100755 index a33997dd1..55fa725bd --- a/snakePipes/__init__.py +++ b/snakePipes/__init__.py @@ -1 +1 @@ -__version__ = '2.1.0' +__version__ = '2.1.1' diff --git a/snakePipes/shared/rules/ATAC.snakefile b/snakePipes/shared/rules/ATAC.snakefile old mode 100644 new mode 100755 index cbbfe5b3b..1ac2c69ce --- a/snakePipes/shared/rules/ATAC.snakefile +++ b/snakePipes/shared/rules/ATAC.snakefile @@ -16,7 +16,7 @@ rule filterFragments: --filterMetrics {output.metrics} \ --maxFragmentLength {params.maxFragmentSize} \ --minFragmentLength {params.minFragmentSize} \ - 2 > {log} + 2> {log} """ @@ -50,9 +50,9 @@ rule filterCoveragePerScaffolds: shell: """ samtools index -@ {threads} {input.bam} 2> {log} samtools idxstats {input.bam} | awk -v cutoff={params.count_cutoff} \'$3 > cutoff\' | cut -f 1 > {output.whitelist} 2>> {log} - samtools view -@ {threads} -bo {output.bam} {input.bam} $(cat {output.whitelist} | paste -sd\' \') 2>> {log} + samtools view -@ {threads} -bo {output.bam} {input.bam} $(cat {output.whitelist} | paste -sd\' \') 2>> {log} samtools index -@ {threads} {output.bam} 2>> {log} - + """