multiqc rule corrected

ATAC-seq_pipeline/Snakefile

@@ -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,
 
 

ATAC-seq_pipeline/rules/pre-processing.smk

@@ -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:

ATAC-seq_pipeline/slurm-1937141.out

-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

ATAC-seq_pipeline/slurm-1937142.out

-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

ATAC-seq_pipeline/slurm-1937143.out

-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

ATAC-seq_pipeline/slurm-1937383.out

-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.