Commit e977d3d4 authored by Wang's avatar Wang
Browse files

multiqc rule corrected

parent a7c2f821
......@@ -50,7 +50,7 @@ wildcard_constraints:
# HMMRATAC will not work with the test dataset.
GFT = WORKING_DIR + "gtf_gene.gtf",
FASTQC = expand(RESULT_DIR + "fastqc/sample_{numbers}_{R}_fastqc.html",numbers = ['8','12','4_7','4_1'], R=['R1', 'R2']),
FASTQC = expand(RESULT_DIR + "fastqc/sample_{numbers}_{R}_fastqc.html",numbers = ['8','12','4_3','4_1'], R=['R1', 'R2']),
FORWARD_READS = expand(WORKING_DIR + "trimmed/{samples}_forward.fastq.gz", samples = SAMPLES),
REVERSE_READS = expand(WORKING_DIR + "trimmed/{samples}_reverse.fastq.gz", samples = SAMPLES),
TRIMMED_FASTQC = expand(RESULT_DIR + "trimmed_fastqc/{samples}_{direction}_fastqc.html", samples = SAMPLES, direction=['forward', 'reverse']),
......@@ -73,7 +73,7 @@ CORRELATION = RESULT_DIR + "correlation/correlation.pdf
HISTOGRAM = RESULT_DIR + "bamPEFragmentSize/histogram.pdf",
PROFILE = RESULT_DIR + "profile/profile_reference_point_genes.pdf",
ANNOTATION = expand(RESULT_DIR + "annotation/{samples}_annotate_homer.txt", samples = SAMPLES),
MULTIQC = RESULT_DIR + "trimmed_fastqc/multiqc_report.html"
MULTIQC = RESULT_DIR + "multiqc/multiqc_report.html"
container: "docker://continuumio/miniconda3:4.4.10"
......@@ -100,7 +100,7 @@ rule all:
CORRELATION,
HISTOGRAM,
PROFILE,
ANNOTATION,
#ANNOTATION,
MULTIQC,
......
......@@ -62,24 +62,24 @@ rule trimmed_fastqc:
rule multiQC:
output:
multiqc = RESULT_DIR + "trimmed_fastqc/multiqc_report.html"
multiqc = RESULT_DIR + "multiqc/multiqc_report.html"
conda:
"../envs/multiqc.yaml"
log:
RESULT_DIR + "logs/multiqc/multiqc.log"
params:
out_folder = RESULT_DIR + "trimmed_fastqc/"
out_folder = RESULT_DIR + "multiqc/"
message:
"Giving summary of fastqc report across samples."
shell:
"multiqc results/trimmed_fastqc -o {params.out_folder} 2>{log}"
"multiqc . -o {params.out_folder} 2>{log}"
rule fastqc:
input:
fwd = expand(DATA_DIR + "sample_{numbers}_R1.fastq.gz", numbers = ['8','12','4_7','4_1']),
rev = expand(DATA_DIR + "sample_{numbers}_R2.fastq.gz", numbers = ['8','12','4_7','4_1'])
fwd = expand(DATA_DIR + "sample_{numbers}_R1.fastq.gz", numbers = ['8','12','4_3','4_1']),
rev = expand(DATA_DIR + "sample_{numbers}_R2.fastq.gz", numbers = ['8','12','4_3','4_1'])
output:
expand(RESULT_DIR + "fastqc/sample_{numbers}_{R}_fastqc.html", numbers = ['8','12','4_7','4_1'], R=['R1', 'R2'])
expand(RESULT_DIR + "fastqc/sample_{numbers}_{R}_fastqc.html", numbers = ['8','12','4_3','4_1'], R=['R1', 'R2'])
log:
expand(RESULT_DIR + "logs/fastqc/{samples}.fastqc.log", samples = SAMPLES)
params:
......
Start time : Tue Feb 16 10:55:12 CET 2021
Building DAG of jobs...
Using shell: /usr/bin/bash
Provided cluster nodes: 30
Singularity containers: ignored
Job counts:
count jobs
1 PCA
1 all
2
[Tue Feb 16 10:55:14 2021]
Job 29: Plotting PCA
plotPCA -in results/bigwigsummary/multiBigwigSummary.npz -o results/PCA/PCA_PLOT.pdf 2>results/logs/bigwigsummary/PCA_PLOT.log
Submitted job 29 with external jobid '1937142'.
[Tue Feb 16 10:55:45 2021]
Finished job 29.
1 of 2 steps (50%) done
[Tue Feb 16 10:55:45 2021]
Job 0: Analysis is complete!
Submitted job 0 with external jobid '1937143'.
[Tue Feb 16 10:55:56 2021]
Finished job 0.
2 of 2 steps (100%) done
Complete log: /exports/humgen/Jianhui/pipeline_test/Snakemake_ATAC_2020/ATAC-seq_pipeline/.snakemake/log/2021-02-16T105513.301902.snakemake.log
End time : Tue Feb 16 10:56:06 CET 2021
Building DAG of jobs...
Using shell: /usr/bin/bash
Provided cores: 8
Rules claiming more threads will be scaled down.
Singularity containers: ignored
Job counts:
count jobs
1 PCA
1
[Tue Feb 16 10:55:17 2021]
Job 0: Plotting PCA
plotPCA -in results/bigwigsummary/multiBigwigSummary.npz -o results/PCA/PCA_PLOT.pdf 2>results/logs/bigwigsummary/PCA_PLOT.log
Activating conda environment: /exports/humgen/Jianhui/pipeline_test/Snakemake_ATAC_2020/ATAC-seq_pipeline/.snakemake/conda/fea33531
[Tue Feb 16 10:55:35 2021]
Finished job 0.
1 of 1 steps (100%) done
Building DAG of jobs...
Using shell: /usr/bin/bash
Provided cores: 8
Rules claiming more threads will be scaled down.
Singularity containers: ignored
Job counts:
count jobs
1 all
1
[Tue Feb 16 10:55:48 2021]
Job 0: Analysis is complete!
[Tue Feb 16 10:55:48 2021]
Finished job 0.
1 of 1 steps (100%) done
Start time : Tue Feb 16 11:05:54 CET 2021
Building DAG of jobs...
Creating conda environment envs/macs2.yaml...
Downloading and installing remote packages.
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment