From 8680abc7ef80d044609914a44e10d69042c0ca6b Mon Sep 17 00:00:00 2001 From: rioualen Date: Fri, 30 Sep 2016 16:14:28 +0200 Subject: [PATCH] minor --- .../workflows/RNA-seq_workflow_SE.py | 105 ++---------------- 1 file changed, 10 insertions(+), 95 deletions(-) diff --git a/scripts/snakefiles/workflows/RNA-seq_workflow_SE.py b/scripts/snakefiles/workflows/RNA-seq_workflow_SE.py index 3a1c6f12..7cb62cb4 100644 --- a/scripts/snakefiles/workflows/RNA-seq_workflow_SE.py +++ b/scripts/snakefiles/workflows/RNA-seq_workflow_SE.py @@ -67,6 +67,12 @@ SAMPLE_IDS = SAMPLES.iloc[:,0] SAMPLE_CONDITIONS = read_table(config["metadata"]["samples"])['condition'] +# Design +#DESIGN = read_table(config["metadata"]["design"]) +#REFERENCE_COND = DESIGN.iloc[:,0] +#TEST_COND = DESIGN.iloc[:,1] + + # Genome & annotations GENOME_VER = config["genome"]["version"] GENOME_DIR = config["dir"]["genome"] + "/" @@ -218,6 +224,7 @@ DEG = expand(DEG_DIR + "{deg}/{prefix}_{deg}_report.html", prefix=PREFIX, deg=DIFFEXPR_TOOLS) +#DEG = expand(expand(DEG_DIR + "{test}_vs_{ref}/{{deg}}/{{prefix}}_{{deg}}_report.html", zip, test=TEST_COND, ref=REFERENCE_COND), prefix=PREFIX, deg=DIFFEXPR_TOOLS) ## ---------------------------------------------------------------- ## Visualization & reports @@ -231,6 +238,8 @@ GENOME_COVERAGE_TDF = expand("{alignment}.tdf", alignment=ALIGNMENT) +GRAPHICS = expand(REPORTS_DIR + "{graph}.png", graph=["dag", "rulegraph"]) + #================================================================# # Rule all # #================================================================# @@ -247,7 +256,7 @@ # SORTED_BAM, \ SORTED_BAM_BAI, \ BAM_STATS, \ - GENOME_COVERAGE_TDF, \ +# GENOME_COVERAGE_TDF, \ ## INFER_TRANSCRIPTS, \ # FEATURE_COUNTS, \ # SARTOOLS_TARGETFILE, \ @@ -256,97 +265,3 @@ params: qsub=config["qsub"] shell: "echo Job done `date '+%Y-%m-%d %H:%M'`" -##================================================================# -## Workflow # -##================================================================# - -### Data import -#IMPORT = expand(SAMPLE_DIR + "{samples}/{samples}.fastq", samples=SAMPLE_IDS) - - -### Genome -#GENOME = config["genome"]["version"] -#GENOME_DIR = config["dir"]["genome"] + config["genome"]["version"] - -#if not os.path.exists(GENOME_DIR): -# os.makedirs(GENOME_DIR) - -#GENOME_FASTA = expand(GENOME_DIR + "/" + GENOME + ".fa") -#GENOME_ANNOTATIONS = expand(GENOME_DIR + "/" + GENOME + ".{ext}", ext=["gff3", "gtf"]) - -### Graphics & reports -#GRAPHICS = expand(REPORTS_DIR + "{graph}.png", graph=["dag", "rulegraph"]) - -##----------------------------------------------------------------# -## Quality control -##----------------------------------------------------------------# - -#RAW_QC = expand(SAMPLE_DIR + "{samples}/{samples}_fastqc/{samples}_fastqc.html", samples=SAMPLE_IDS) - - -##----------------------------------------------------------------# -## Trimming -##----------------------------------------------------------------# - -##TRIMMER="sickle-q" + config["sickle"]["threshold"] -##TRIMMING=expand(SAMPLE_DIR + "{samples}/{samples}_{trimmer}", samples=SAMPLE_IDS, trimmer=TRIMMER) -##TRIM = expand("{trimming}.fastq", trimming=TRIMMING) - -##TRIM_QC = expand(SAMPLE_DIR + "{samples}/{samples}_{trimmer}_fastqc/{samples}_{trimmer}_fastqc.html", samples=SAMPLE_IDS, trimmer=TRIMMER) - -##QC = RAW_QC + TRIM_QC - - -##----------------------------------------------------------------# -## Alignment -##----------------------------------------------------------------# - - -#ALIGNER=["bowtie2", "bowtie", "subread"] -#INDEX = expand(GENOME_DIR + "/{aligner}/" + GENOME + ".fa", aligner=ALIGNER) - -#ALIGNER.append("tophat") - -#ALIGNMENT=expand(SAMPLE_DIR + "{samples}/{samples}_{aligner}", samples=SAMPLE_IDS, aligner=ALIGNER) -#MAPPING = expand("{alignment}.bam", alignment=ALIGNMENT) - -#BAM_STATS = expand("{alignment}_bam_stats.txt", alignment=ALIGNMENT) - -##SORTED_BAM = expand("{alignment}_sorted_pos.bam", alignment=ALIGNMENT) - -##----------------------------------------------------------------# -## RNA-seq analysis -##----------------------------------------------------------------# - - -#INFER_TRANSCRIPTS = expand("{alignment}_cufflinks/transcripts.gtf", alignment=ALIGNMENT) - - -#FEATURE_COUNTS = expand("{alignment}_featureCounts.txt", alignment=ALIGNMENT) - -#SARTOOLS_TARGETFILE = expand(DEG_DIR + "{aligner}_SARTools_design.txt", aligner=ALIGNER) - -#DEG = expand(DEG_DIR + "{aligner}_{deg}_report.html", aligner=ALIGNER, deg=["DESeq2", "edgeR"]) - - -#GENOME_COVERAGE = expand("{alignment}.bedgraph.gz", alignment=ALIGNMENT) - -### ---------------------------------------------------------------- -### Visualization -### ---------------------------------------------------------------- - -##VISU = expand(PEAKS_DIR + "igv_session.xml") - -##================================================================# -## Rule all # -##================================================================# - -#rule all: -# """ -# Run all the required analyses. -# """ -# input: GRAPHICS, BAM_STATS, FEATURE_COUNTS, INFER_TRANSCRIPTS, GENOME_COVERAGE, SARTOOLS_TARGETFILE, DEG -# params: qsub=config["qsub"] -# shell: "echo Job done `date '+%Y-%m-%d %H:%M'`" - -##sed -n FEATURE_COUNTS, '/digraph/,$p'