diff --git a/docs/usage/output.rst b/docs/usage/output.rst
index 8bcd2f8f..f01cc3f5 100644
--- a/docs/usage/output.rst
+++ b/docs/usage/output.rst
@@ -58,7 +58,7 @@ Assembly
 
 Besides the `reports/assembly_report.html`_ this rule outputs the following files per sample:
 
-  - ``{sample}/{sample}_contigs.fasta``
+  - ``Assembly/fasta/{sample}.fasta``
   - ``{sample}/sequence_alignment/{sample}.bam``
   - ``{sample}/assembly/contig_stats/final_contig_stats.txt``
 
diff --git a/workflow/rules/assemble.smk b/workflow/rules/assemble.smk
index ea88f14c..db2bd69f 100644
--- a/workflow/rules/assemble.smk
+++ b/workflow/rules/assemble.smk
@@ -597,10 +597,11 @@ rule finalize_contigs:
     input:
         "{sample}/assembly/{sample}_final_contigs.fasta",
     output:
-        "{sample}/{sample}_contigs.fasta",
+        "Assembly/fasta/{sample}.fasta",
     threads: 1
-    run:
-        os.symlink(os.path.relpath(input[0], os.path.dirname(output[0])), output[0])
+    shell:
+        "cp {input} {output}"
+        
 
 
 rule calculate_contigs_stats:
@@ -624,7 +625,7 @@ rule calculate_contigs_stats:
 rule align_reads_to_final_contigs:
     input:
         query=get_quality_controlled_reads,
-        target="{sample_contigs}/{sample_contigs}_contigs.fasta",
+        target="Assembly/fasta/{sample_contigs}.fasta",
     output:
         bam="{sample_contigs}/sequence_alignment/{sample}.bam",
     params:
diff --git a/workflow/rules/patch.smk b/workflow/rules/patch.smk
index 3daae3fd..3fe28e6e 100644
--- a/workflow/rules/patch.smk
+++ b/workflow/rules/patch.smk
@@ -2,11 +2,13 @@ localrules: move_qc_reads, copy_assembly
 
 # Rules that are usefull temporarily to update to new version of atlas
 
+
+ruleorder: move_qc_reads > qcreads
 rule move_qc_reads:
     input:
         "{sample}/sequence_quality_control/{sample}_clean_{fraction}.fastq.gz"
     output:
-        "QCreads/{sample}_{fraction}.fastq.gz"
+        "QC/reads/{sample}_{fraction}.fastq.gz"
     shell:
         "mv {input} {output}"
 
diff --git a/workflow/rules/qc.smk b/workflow/rules/qc.smk
index cd792ca3..10cf48ce 100644
--- a/workflow/rules/qc.smk
+++ b/workflow/rules/qc.smk
@@ -417,12 +417,9 @@ if not SKIP_QC:
             unpack(get_ribosomal_rna_input),
         output:
             expand(
-                "{{sample}}/sequence_quality_control/{{sample}}_{step}_{fraction}.fastq.gz",
-                step=PROCESSED_STEPS[-1],
+                "QC/reads/{{sample}}_{fraction}.fastq.gz",
                 fraction=MULTIFILE_FRACTIONS,
             ),
-        params:
-            sample_table="samples.tsv",
         threads: 1
         run:
             import shutil
diff --git a/workflow/rules/sample_table.smk b/workflow/rules/sample_table.smk
index ff0e05a3..cb3eb787 100644
--- a/workflow/rules/sample_table.smk
+++ b/workflow/rules/sample_table.smk
@@ -175,7 +175,7 @@ def get_quality_controlled_reads(wildcards, include_se=False):
     except FileNotInSampleTableException:
         # return files as named by atlas pipeline
         return expand(
-            "{sample}/sequence_quality_control/{sample}_QC_{fraction}.fastq.gz",
+            "QC/reads/{sample}_{fraction}.fastq.gz",
             fraction=Fractions,
             sample=wildcards.sample,
         )
@@ -194,5 +194,5 @@ def get_assembly(wildcards):
     except FileNotInSampleTableException:
         # return files as named by atlas pipeline
 
-        return "{sample}/{sample}_contigs.fasta".format(sample=wildcards.sample )
+        return "Assembly/fasta/{sample}.fasta".format(sample=wildcards.sample )