drop module

metagenome-atlas · Oct 9, 2023 · 387c3b5 · 387c3b5
1 parent fb43561
commit 387c3b5
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Showing 3 changed files with 3 additions and 16 deletions.
diff --git a/atlas/init/atlas_init.py b/atlas/init/atlas_init.py
@@ -59,7 +59,7 @@ def prepare_sample_table_for_atlas(
     if not reads_are_QC:
         for f in fractions:
             sample_table[f"Reads_QC_{f}"] = (
-                f"QCreads/" + sample_table.index + f"_{f}.fastq.gz"
+                f"QC/reads/" + sample_table.index + f"_{f}.fastq.gz"
             )
 
     sample_table["Assembly"] = "Assembly/fasta/" + sample_table.index + ".fasta"

diff --git a/test/test_local.sh b/test/test_local.sh
@@ -30,9 +30,9 @@ rm -f $WD/samples.tsv
 #
 atlas init $reads_dir -w $WD 
 
-atlas run None screen -w $WD qc  $snakemake_args
+#atlas run None screen -w $WD  $snakemake_args
 
-echo "\n\nFinished screen\n\n"
+# echo "\n\nFinished screen\n\n"
 
 atlas run -w $WD qc  $snakemake_args
 

diff --git a/workflow/rules/qc.smk b/workflow/rules/qc.smk
@@ -130,19 +130,6 @@ rule get_read_stats:
     script:
         "../scripts/get_read_stats.py"
 
-use rule get_read_stats as get_gc_read_stats with:
-    input:
-        get_quality_controlled_reads
-    output:
-        "{sample}/sequence_quality_control/read_stats/QC.zip",
-        read_counts=temp(
-            "{sample}/sequence_quality_control/read_stats/QC_read_counts.tsv"
-        ),
-    log:
-        "{sample}/logs/QC/read_stats/QC.log",
-    params:
-        folder=lambda wc, output: os.path.splitext(output[0])[0],
-
 if not SKIP_QC:
     if config.get("deduplicate", True):
         PROCESSED_STEPS.append("deduplicated")