goes back to older dir structure setup for rename-config

workflow/rules/aggregate_results.smk

@@ -8,7 +8,7 @@ rule multiqc_by_sample_initial_pass:
         OUT_DIR / "{sample}" / "qc" / "verifyBamID" / "{sample}.Ancestry",
         OUT_DIR / "{sample}" / "qc" / "bcftools-stats" / "{sample}.bcftools.stats",
         multiqc_config="configs/multiqc_config.yaml",
-        rename_config=PROJECT_PATH / "{sample}" / "qc" / "multiqc_initial_pass" / "{sample}_rename_config.tsv",
+        rename_config=PROJECT_PATH / "{sample}" / "qc" / "multiqc_initial_pass" / "multiqc_sample_rename_config"  / "{sample}_rename_config.tsv",
     output:
         OUT_DIR / "{sample}" / "qc" / "multiqc_initial_pass" / "{sample}_multiqc.html",
         OUT_DIR / "{sample}" / "qc" / "multiqc_initial_pass" / "{sample}_multiqc_data" / "multiqc_general_stats.txt",
@@ -18,7 +18,7 @@ rule multiqc_by_sample_initial_pass:
     message:
         "Aggregates QC results using multiqc. First pass. Output will be used for the internal QC checkup. Sample: {wildcards.sample}"
     params:
-        # multiqc uses fastq's filenames to identify sample names. We renamed them based on units.tsv file,
+        # multiqc uses fastq's filenames to identify sample names. Rename them to in-house names,
         # using custom rename config file
         extra=lambda wildcards, input: f"--config {input.multiqc_config} --sample-names {input.rename_config}",
     wrapper:
@@ -69,7 +69,7 @@ rule multiqc_by_sample_final_pass:
         OUT_DIR / "{sample}" / "qc" / "bcftools-stats" / "{sample}.bcftools.stats",
         OUT_DIR / "{sample}" / "qc" / "qc_checkup" / "qc_checkup_overall_summary.yaml",
         multiqc_config="configs/multiqc_config.yaml",
-        rename_config=PROJECT_PATH / "{sample}" / "qc" / "multiqc_initial_pass" / "{sample}_rename_config.tsv",
+        rename_config=PROJECT_PATH / "{sample}" / "qc" / "multiqc_initial_pass" / "multiqc_sample_rename_config"  / "{sample}_rename_config.tsv",
         qc_config="configs/qc_checkup/qc_checkup_config.yaml",
     output:
         OUT_DIR / "{sample}" / "qc" / "multiqc_final_pass" / "{sample}_multiqc.html",
@@ -78,7 +78,7 @@ rule multiqc_by_sample_final_pass:
     message:
         "Aggregates QC results using multiqc. Final pass, where QC checkup results are also aggregated"
     params:
-        # multiqc uses fastq's filenames to identify sample names. We renamed them based on units.tsv file,
+        # multiqc uses fastq's filenames to identify sample names. Rename them to in-house names,
         # using custom rename config file
         extra=lambda wildcards, input: f"--config {input.multiqc_config} --sample-names {input.rename_config}",
     wrapper:
@@ -92,7 +92,7 @@ localrules:
 
 rule aggregate_sample_rename_configs:
     input:
-        expand(PROJECT_PATH / "{sample}" / "qc" / "multiqc_initial_pass" / "{sample}_rename_config.tsv", sample=SAMPLES),
+        expand(PROJECT_PATH / "{sample}" / "qc" / "multiqc_initial_pass" / "multiqc_sample_rename_config"  / "{sample}_rename_config.tsv", sample=SAMPLES),
     output:
         OUT_DIR / "project_level_qc" / "multiqc" / "aggregated_rename_configs.tsv",
     message:
@@ -129,7 +129,7 @@ rule multiqc_aggregation_all_samples:
     message:
         "Running multiqc for all samples"
     params:
-        # multiqc uses fastq's filenames to identify sample names. We renamed them based on units.tsv file,
+        # multiqc uses fastq's filenames to identify sample names. Rename them to in-house names,
         # using custom rename config file
         extra=(
             lambda wildcards, input: f'--config {input.multiqc_config} \