Add a WIP notice for explore

Author: remiolsen

README.md

@@ -11,7 +11,7 @@ Anglerfish is a tool designed to demultiplex Illumina libraries sequenced on Oxf
 flowcells. The primary purpose for this would be to do QC, i.e. to check pool balancing, assess
 contamination, library insert sizes and so on.
 
-For more information on how this can be used, please see this [poster](docs/AGBT_poster_20200214.pdf).
+For more information please read the [documentation](https://anglerfish-dev.readthedocs.io/en/latest/index.html) or see this [poster](docs/AGBT_poster_20200214.pdf).
 
 ## Installation
 

docs/anglerfish-explore.md

@@ -1 +1,51 @@
 # Explore demultiplexing, the experimental method
+
+```{admonition} Note
+  :kind: warning
+  This mode of anglerfish work-in-progress and as such is not feature complete and might give sub-optimal results
+```
+
+This is a way of running anglerfish without using a samplesheet. The functionality is however quite different from `anglerfish run`
+It will attempt, using read alignment, to find which adapter types are present in a given pool and their index length(s).
+
+The basic usage of `anglerfish explore` expects two arguments, one for a single input fastq file `-f` and one for the output directory `-o`. Example shown for a pool where it finds `truseq_dual` adapters with 8+8 bp index length.
+
+```
+anglerfish explore -f fastq_passed/concat.fastq.gz -o explore
+INFO:explore:Running anglerfish explore
+INFO:explore:Run uuid 6b1c9b21-029f-4fc3-b28a-9214c776048a
+INFO:explore:Aligning illumina_ud
+INFO:explore:Aligning truseq
+INFO:explore:Aligning truseq_dual
+INFO:explore:Aligning truseq_umi
+INFO:explore:Aligning nextera_legacy
+INFO:explore:Aligning nextera_dual
+INFO:explore:Parsing illumina_ud
+INFO:explore:illumina_ud:i5 had 0 good hits.
+INFO:explore:illumina_ud:i7 had 0 good hits.
+INFO:explore:Adaptor illumina_ud is excluded from the analysis
+INFO:explore:Parsing truseq
+INFO:explore:truseq:i5 had 0 good hits.
+INFO:explore:truseq:i7 had 5810 good hits.
+INFO:explore:Adaptor truseq is excluded from the analysis
+INFO:explore:Parsing truseq_dual
+INFO:explore:truseq_dual:i5 had 779 good hits.
+INFO:explore:truseq_dual:i7 had 5810 good hits.
+INFO:explore:Adaptor truseq_dual is included in the analysis
+INFO:explore:Parsing truseq_umi
+INFO:explore:truseq_umi:i5 had 779 good hits.
+INFO:explore:truseq_umi:i7 had 0 good hits.
+INFO:explore:Adaptor truseq_umi is excluded from the analysis
+INFO:explore:Parsing nextera_legacy
+INFO:explore:nextera_legacy:i5 had 0 good hits.
+INFO:explore:nextera_legacy:i7 had 0 good hits.
+INFO:explore:Adaptor nextera_legacy is excluded from the analysis
+INFO:explore:Parsing nextera_dual
+INFO:explore:nextera_dual:i5 had 0 good hits.
+INFO:explore:nextera_dual:i7 had 0 good hits.
+INFO:explore:Adaptor nextera_dual is excluded from the analysis
+INFO:explore:truseq_dual:i5 had 779 good hits with median insert length 8.0
+INFO:explore:truseq_dual:i5 insert length histogram saved explore/truseq_dual_i5.hist.csv
+INFO:explore:truseq_dual:i7 had 5810 good hits with median insert length 8.0
+INFO:explore:truseq_dual:i7 insert length histogram saved explore/truseq_dual_i7.hist.csv
+```

docs/index.rst

@@ -12,4 +12,3 @@ Contents
    anglerfish
    anglerfish-run
    anglerfish-explore
-   troubleshooting