add condition to fix handling of one file

pdimens · Jun 28, 2024 · 8ab36dc · 8ab36dc
1 parent 0c0aa72
commit 8ab36dc
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Showing 3 changed files with 6 additions and 6 deletions.
diff --git a/src/harpy/snakefiles/align-bwa.smk b/src/harpy/snakefiles/align-bwa.smk
@@ -282,15 +282,15 @@ rule report_bx:
     message: 
         "Summarizing all barcode information from alignments"
     script:
-        "report/BxAlignStats.Rmd"
+        "report/AlignBxStats.Rmd"
 
 rule log_workflow:
     default_target: True
     input:
         bams = collect(outdir + "/{sample}.{ext}", sample = samplenames, ext = ["bam", "bam.bai"]),
         reports = collect(outdir + "/reports/{sample}.html", sample = samplenames) if not skipreports else [],
         agg_report = outdir + "/reports/bwa.stats.html" if not skipreports else [],
-        bx_report = outdir + "/reports/barcodes.summary.html" if not skipreports else []
+        bx_report = outdir + "/reports/barcodes.summary.html" if (not skipreports or len(samplenames) == 1) else []
     params:
         quality = config["alignment_quality"],
         extra   = extra

diff --git a/src/harpy/snakefiles/align-ema.smk b/src/harpy/snakefiles/align-ema.smk
@@ -370,15 +370,15 @@ rule report_bx:
     message: 
         "Summarizing all barcode information from alignments"
     script:
-        "report/BxAlignStats.Rmd"
+        "report/AlignBxStats.Rmd"
 
 rule log_workflow:
     default_target: True
     input:
         bams = collect(outdir + "/{sample}.{ext}", sample = samplenames, ext = [ "bam", "bam.bai"] ),
         cov_report = collect(outdir + "/reports/{sample}.html", sample = samplenames) if not skipreports else [],
         agg_report = f"{outdir}/reports/ema.stats.html" if not skipreports else [],
-        bx_report = outdir + "/reports/barcodes.summary.html" if not skipreports else []
+        bx_report = outdir + "/reports/barcodes.summary.html" if (not skipreports or len(samplenames) == 1) else []
     params:
         beadtech = "-p" if platform == "haplotag" else f"-w {whitelist}"
     message:

diff --git a/src/harpy/snakefiles/align-strobealign.smk b/src/harpy/snakefiles/align-strobealign.smk
@@ -281,15 +281,15 @@ rule report_bx:
     message: 
         "Summarizing all barcode information from alignments"
     script:
-        "report/BxAlignStats.Rmd"
+        "report/AlignBxStats.Rmd"
 
 rule log_workflow:
     default_target: True
     input: 
         bams = collect(outdir + "/{sample}.{ext}", sample = samplenames, ext = ["bam","bam.bai"]),
         samtools =  outdir + "/reports/strobealign.stats.html" if not skipreports else [] ,
         reports = collect(outdir + "/reports/{sample}.html", sample = samplenames) if not skipreports else [],
-        bx_report = outdir + "/reports/barcodes.summary.html" if not skipreports else []
+        bx_report = outdir + "/reports/barcodes.summary.html" if (not skipreports or len(samplenames) == 1) else []
     params:
         readlen = readlen,
         quality = config["quality"],