add patch to move reads and assembly

workflow/Snakefile

@@ -51,6 +51,7 @@ include: "rules/sra.smk"
 include: "rules/gtdbtk.smk"
 include: "rules/cobinning.smk"
 include: "rules/strains.smk"
+include: "rules/patch.smk"
 
 
 CONDAENV = "envs"  # overwrite definition in download.smk

workflow/rules/patch.smk

@@ -0,0 +1,20 @@
+localrules: move_qc_reads, copy_assembly
+
+# Rules that are usefull temporarily to update to new version of atlas
+
+rule move_qc_reads:
+    input:
+        "{sample}/sequence_quality_control/{sample}_clean_{fraction}.fastq.gz"
+    output:
+        "QCreads/{sample}_{fraction}.fastq.gz"
+    shell:
+        "mv {input} {output}"
+
+rule copy_assembly:
+    input:
+        "{sample}/{sample}_contigs.fasta"
+    output:
+        "Assembly/fasta/{sample}.fasta"
+    shell:
+        "cp {input} {output}"
+