cleaner multiqc call

pdimens · Jun 27, 2024 · 28bce57 · 28bce57
1 parent 452d1c8
commit 28bce57
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Showing 5 changed files with 27 additions and 20 deletions.
diff --git a/src/harpy/snakefiles/align-bwa.smk b/src/harpy/snakefiles/align-bwa.smk
@@ -261,15 +261,16 @@ rule report_samtools:
     output: 
         outdir + "/reports/bwa.stats.html"
     params:
-        outdir
+        outdir = f"{outdir}/reports/data/samtools_stats {outdir}/reports/data/samtools_flagstat",
+        options = "--no-version-check --force --quiet --no-data-dir",
+        title = "--title \"Basic Alignment Statistics\"",
+        comment = "--comment \"This report aggregates samtools stats and samtools flagstats results for all alignments. Samtools stats ignores alignments marked as duplicates.\""
     conda:
         f"{envdir}/qc.yaml"
     message:
         "Summarizing samtools stats and flagstat"
     shell:
-        """
-        multiqc {params}/reports/data/samtools_stats {params}/reports/data/samtools_flagstat --no-version-check --force --quiet --title "General Alignment Statistics" --comment "This report aggregates samtools stats and samtools flagstats results for all alignments. Samtools stats ignores alignments marked as duplicates." --no-data-dir --filename {output} 2> /dev/null
-        """
+        "multiqc {params} --filename {output} 2> /dev/null"
 
 rule report_bx:
     input:

diff --git a/src/harpy/snakefiles/align-ema.smk b/src/harpy/snakefiles/align-ema.smk
@@ -349,15 +349,16 @@ rule report_samtools:
     output: 
         outdir + "/reports/ema.stats.html"
     params:
-        outdir
+        outdir = f"{outdir}/reports/data/samtools_stats {outdir}/reports/data/samtools_flagstat",
+        options = "--no-version-check --force --quiet --no-data-dir",
+        title = "--title \"Basic Alignment Statistics\"",
+        comment = "--comment \"This report aggregates samtools stats and samtools flagstats results for all alignments. Samtools stats ignores alignments marked as duplicates.\""
     conda:
         f"{envdir}/qc.yaml"
     message:
         "Summarizing samtools stats and flagstat"
     shell:
-        """
-        multiqc {outdir}/reports/data/samtools_stats {outdir}/reports/data/samtools_flagstat --no-version-check --force --quiet --title "General Alignment Statistics" --comment "This report aggregates samtools stats and samtools flagstats results for all alignments. Samtools stats ignores alignments marked as duplicates." --no-data-dir --filename {output} 2> /dev/null
-        """
+        "multiqc {params} --filename {output} 2> /dev/null"
 
 rule report_bx:
     input:

diff --git a/src/harpy/snakefiles/align-strobealign.smk b/src/harpy/snakefiles/align-strobealign.smk
@@ -260,15 +260,16 @@ rule report_samtools:
     output: 
         outdir + "/reports/strobealign.stats.html"
     params:
-        outdir
+        outdir = f"{outdir}/reports/data/samtools_stats {outdir}/reports/data/samtools_flagstat",
+        options = "--no-version-check --force --quiet --no-data-dir",
+        title = "--title \"Basic Alignment Statistics\"",
+        comment = "--comment \"This report aggregates samtools stats and samtools flagstats results for all alignments. Samtools stats ignores alignments marked as duplicates.\""
     conda:
         f"{envdir}/qc.yaml"
     message:
         "Summarizing samtools stats and flagstat"
     shell:
-        """
-        multiqc {params}/reports/data/samtools_stats {params}/reports/data/samtools_flagstat --no-version-check --force --quiet --title "Basic Alignment Statistics" --comment "This report aggregates samtools stats and samtools flagstats results for all alignments. Samtools stats ignores alignments marked as duplicates." --no-data-dir --filename {output} 2> /dev/null
-        """
+        "multiqc  {params} --filename {output} 2> /dev/null"
 
 rule report_bx:
     input:

diff --git a/src/harpy/snakefiles/demultiplex.gen1.smk b/src/harpy/snakefiles/demultiplex.gen1.smk
@@ -184,15 +184,16 @@ rule qc_report:
     output:
         outdir + "/reports/demultiplex.QC.html"
     params:
-        outdir + "/logs/"
+        logdir = outdir + "/logs/",
+        options = "--no-version-check --force --quiet --no-data-dir",
+        title = "--title \"QC for Demultiplexed Samples\"",
+        comment = "--comment \"This report aggregates the QC results created by falco.\""
     conda:
         f"{envdir}/qc.yaml"
     message:
         "Creating final demultiplexing QC report"
     shell:
-        """
-        multiqc {params} --no-version-check --force --quiet --title "QC for Demultiplexed Samples" --comment "This report aggregates the QC results created by falco." --no-data-dir --filename {output} 2> /dev/null
-        """
+        "multiqc {params} --filename {output} 2> /dev/null"
 
 rule log_workflow:
     default_target: True

diff --git a/src/harpy/snakefiles/qc.smk b/src/harpy/snakefiles/qc.smk
@@ -114,15 +114,18 @@ rule create_report:
     log:
         outdir + "/logs/mutliqc.log"
     params:
-        outdir
+        logdir = f"{outdir}/reports/data/fastp/",
+        module = "-m fastp",
+        options = "--no-version-check --force --quiet --no-data-dir",
+        title = "--title \"QC Summary\"",
+        comment = "--comment \"This report aggregates trimming and quality control metrics reported by fastp.\""
+
     conda:
         f"{envdir}/qc.yaml"
     message:
         "Aggregating fastp reports"
     shell: 
-        """
-        multiqc {params}/reports/data/fastp/ -m fastp --force --filename {output} --quiet --title "QC Summary" --comment "This report aggregates trimming and quality control metrics reported by fastp" --no-data-dir 2> {log}
-        """
+        "multiqc {params} --filename {output} 2> {log}"
 
 rule log_workflow:
     default_target: True