Description of output files. Part II

docs/output.md

@@ -41,11 +41,11 @@ This subworkflow generates a KMER database and coverage model used in [PURGE_DUP
 <details markdown="1">
   <summary>Output files</summary>
 
-  - <code>\*hifiasm\*/*p_ctg.[g]fa</code>
+  - <code>.\*hifiasm.\*/.*p_ctg.[g]fa</code>
     - primary assembly in GFA and FASTA format; for more details refer to [hifiasm output](https://hifiasm.readthedocs.io/en/latest/interpreting-output.html) 
-  - <code>\*hifiasm\*/a_ctg.[g]fa</code>
+  - <code>.\*hifiasm.\*/.*a_ctg.[g]fa</code>
     - haplotigs in GFA and FASTA format; for more details refer to [hifiasm output](https://hifiasm.readthedocs.io/en/latest/interpreting-output.html)
-  - <code>\*hifiasm\*/*bin</code>
+  - <code>.\*hifiasm.\*/.*bin</code>
     - internal binary hifiasm files; for more details refer [here](https://hifiasm.readthedocs.io/en/latest/faq.html#id12)
 
 </details>
@@ -60,9 +60,9 @@ In case hifiasm HiC mode is switched on, it is performed as an extra step with r
 <details markdown="1">
   <summary>Output files</summary>
 
-  - <code>\*.hifiasm.\*/purged.fa</code>
+  - <code>\*.hifiasm..\*/purged.fa</code>
     - purged primary contigs
-  - <code>\*.hifiasm.\*/purged.htigs.fa</code>
+  - <code>\*.hifiasm..\*/purged.htigs.fa</code>
     - haplotigs after purging  
   - other files from the purge_dups pipeline
     - for details refer [here](https://github.com/dfguan/purge_dups)
@@ -79,13 +79,13 @@ The subworkflow relies on kmer coverage model to identify coverage thresholds. F
 <details markdown="1">
   <summary>Output files</summary>
 
-  - <code>polishing/*consensus.fa</code>
+  - <code>\*.hifiasm..\*/polishing/.*consensus.fa</code>
     - polished joined primary and haplotigs assembly
-  - <code>polishing/merged.vcf.gz</code>
+  - <code>\*.hifiasm..\*/polishing/merged.vcf.gz</code>
     - unfiltered variants
-  - <code>polishing/merged.vcf.gz.tbi</code>
+  - <code>\*.hifiasm..\*/polishing/merged.vcf.gz.tbi</code>
     - index file
-  - <code>polishing/refdata-*</code>
+  - <code>\*.hifiasm..\*/polishing/refdata-*</code>
     - Longranger assembly indices
 
 
@@ -100,19 +100,10 @@ This subworkflow uses read mapping of the Illumina 10X short read data to fix sh
 <details markdown="1">
   <summary>Output files</summary>
 
-  - <code>bed</code>
+  - <code>\*.hifiasm..\*/scaffolding/.*_merged_sorted.bed</code>
     - bed file obtained from merged mkdup bam
-  - <code>cram</code>
-    - reads mapped to the reference
-  - <code>crai</code>
-    - index file for the mapped cram
-  - <code>stats</code>
-    - see [`CONVERT_STATS`](#convert_stats) output section
-  - <code>idxstats</code>
-    - output of samtools stats 
-  - <code>flagstat</code>
-    - output of samtools flagstat
-
+  - <code>\*.hifiasm..\*/scaffolding/.*mkdup.bam</code>
+    - final read mapping bam with mapped reads  
 </details>
 
 This subworkflow implements alignment of the Illumina HiC short reads to the primary assembly. Uses [`CONVERT_STATS`](#convert_stats) as internal subworkflow to calculate read mapping stats.</p> 
@@ -124,11 +115,11 @@ This subworkflow implements alignment of the Illumina HiC short reads to the pri
 
 <details markdown="1">
   <summary>Output files</summary>
-  - <code>stats</code>
+  - <code>\*.hifiasm..\*/scaffolding/.*.stats</code>
     - output of samtools stats 
-  - <code>idxstats</code>
+  - <code>\*.hifiasm..\*/scaffolding/.*.idxstats</code>
     - output of samtools idxstats
-  - <code>flagstat</code>
+  - <code>\*.hifiasm..\*/scaffolding/.*.flagstat</code>
     - output of samtools flagstat  
 </details>
 
@@ -138,8 +129,18 @@ This subworkflow produces statistcs for a bam file containing read mapping. It i
 <details markdown="1">
   <summary>Output files</summary>
 
-  - <code>scaffolds</code>
+  - <code>\*.hifiasm..\*/scaffolding/yahs/out.break.yahs/out_scaffolds_final.fa</code>
     - scaffolds in FASTA format
+  - <code>\*.hifiasm..\*/scaffolding/yahs/out.break.yahs/out_scaffolds_final.agp</code>
+    - coordinates of contigs relative to scaffolds
+  - <code>\*.hifiasm..\*/scaffolding/yahs/out.break.yahs/alignments_sorted.txt</code>
+    - Alignments for Juicer in text format
+  - <code>\*.hifiasm..\*/scaffolding/yahs/out.break.yahs/yahs_scaffolds.hic</code>
+    - Juicer HiC map
+  - <code>\*.hifiasm..\*/scaffolding/yahs/out.break.yahs/*cool</code>
+    - HiC map for cooler
+  - <code>\*.hifiasm..\*/scaffolding/yahs/out.break.yahs/*.FullMap.png</code>
+    - Pretext snapshot
 
 </details>
 The subworkflow performs scaffolding of the primary contigs using HiC mapping generated in [`HIC_MAPPING`](hic_mapping). It also performs some postprocessing steps such as generating cooler and pretext files</p> 
@@ -151,11 +152,11 @@ The subworkflow performs scaffolding of the primary contigs using HiC mapping ge
 <details markdown="1">
   <summary>Output files</summary>
 
-  - <code>*.assembly_summary</code>
+  - <code>.*.assembly_summary</code>
     - numeric statistics for pri and alt sequences
-  - <code>*ccs.merquryk</code>
+  - <code>.*ccs.merquryk</code>
     - folder with merqury plots and kmer statistics
-  - <code>*busco</code>
+  - <code>.*busco</code>
     - folder with BUSCO results
 
 </details>
@@ -169,11 +170,11 @@ This subworkflow is used to evaluate the quality of sequences. It is performed a
 <details markdown="1">
   <summary>Output files</summary>
 
-  - <code>final_mitogenome.fasta</code>
+  - <code>\*.hifiasm.\*/mito..*/final_mitogenome.fasta</code>
     - organelle assembly
-  - <code>final_mitogenome.[gb,gff]</code>
+  - <code>\*.hifiasm.\*/mito..*/final_mitogenome.[gb,gff]</code>
     - organelle gene annotation
-  - <code>contigs_stats.tsv</code>
+  - <code>\*.hifiasm.\*/mito..*/contigs_stats.tsv</code>
     - summary of mitochondrial findings
   - output also includes other output files produced by MitoHiFi