updating consensus pipeline to successfully process IAV through module 3

.dockerignore

@@ -0,0 +1 @@
+**/test-data

.gitattributes

@@ -0,0 +1,11 @@
+# Set the default behavior, in case people don't have core.autocrlf set.
+# This will convert to native OS line ending on checkout and commit as LF (!CRLF) on commit
+* text=auto
+# Denote all files that are truly binary and should not be modified.
+*.png binary
+*.jpg binary
+*.jpeg binary
+*.xz binary
+*.7z binary
+*.gz binary
+*.zip binary

Dockerfile

@@ -131,8 +131,12 @@ RUN conda env create -f /root/idies/workspace/covid19/code/ncov/environment.yml
 COPY ./ /root/idies/workspace/covid19/code/ncov/
 RUN cp -r /root/idies/workspace/covid19/code/ncov/covid19 /root/idies/workspace/ \
     && ln -s /root/idies/workspace/covid19/code/ncov/igv-genomes /root/idies/workspace/covid19 \
-    && cp /root/idies/workspace/covid19/code/ncov/barcode_arrs_nb96.cfg /root/idies/workspace/covid19/code/ont-guppy-cpu/data/barcoding/ \
-    && cp /root/idies/workspace/covid19/code/ncov/barcodes_masked.fasta /root/idies/workspace/covid19/code/ont-guppy-cpu/data/barcoding/
+    && cp /root/idies/workspace/covid19/code/ncov/config/guppy/barcode_arrs_pcr12-JHUAPL_IAV.cfg /root/idies/workspace/covid19/code/ont-guppy-cpu/data/barcoding/ \
+    && cp /root/idies/workspace/covid19/code/ncov/config/guppy/barcode_arrs_nb96.cfg /root/idies/workspace/covid19/code/ont-guppy-cpu/data/barcoding/ \
+    && cp /root/idies/workspace/covid19/code/ncov/config/guppy/barcodes_masked.fasta /root/idies/workspace/covid19/code/ont-guppy-cpu/data/barcoding/ \
+    && cp /root/idies/workspace/covid19/code/ncov/config/guppy/barcodes_masked-JHUAPL_IAV.fasta /root/idies/workspace/covid19/code/ont-guppy-cpu/data/barcoding/ \
+    && cp -r /root/idies/workspace/covid19/code/ncov/primer_schemes/IAV-H1 /root/idies/workspace/covid19/code/artic-ncov2019/primer_schemes/ \
+    && cp -r /root/idies/workspace/covid19/code/ncov/primer_schemes/IAV-H3 /root/idies/workspace/covid19/code/artic-ncov2019/primer_schemes/
 
 #################################################################
 # copy 13-gene genome.json over into RAMPART directory (which has a 9-gene file by default)

config/guppy/barcode_arrs_pcr12-JHUAPL_IAV.cfg

@@ -0,0 +1,56 @@
+####################
+#
+# barcode_arrs_JHUAPL-IAV_nb96.cfg
+#
+#  Created on: February 12, 2021
+#  Derived from: barcode_arrs_nb96.cfg
+#  Updated by: JHU/APL
+#  Proprietary and confidential information of Oxford Nanopore Technologies, Limited
+#  All rights reserved; (c)2017: Oxford Nanopore Technologies, Limited
+#
+####################
+#
+#  2-Barcode Arrangement Variant 1:
+#  
+#         BCXX_1st                           BCXX_2nd
+#  FWD  >-=====------------------------------=====-\
+#                                                   |
+#  REV  <-=====------------------------------=====-/
+#         BCXX_1st                           BCXX_2nd
+#
+#  leads to basecall BCXX_1st_FWD----------BCXX_2nd_REV
+#
+###
+#
+#  2-Barcode Arrangement Variant 2:
+#
+#     BCXX_1st                           BCXX_2nd
+#   /-=====------------------------------=====->  REV
+#  |
+#   \-=====------------------------------=====-<  FWD
+#     BCXX_1st                           BCXX_2nd
+#
+#  leads to basecall BCXX_2nd_FWD----------BCXX_1st_REV
+#
+#  the sequences BCXX_1st and BCXX_2nd will be equal
+#  for most of their parts, especially for the main barcode.
+#  They will usually only differ in the rear spacer between
+#  barcode and (actual) strand.
+#
+####################
+
+[loading_options]
+barcodes_filename = barcodes_masked-JHUAPL_IAV.fasta
+double_variants_frontrear = true
+
+# ############### Native barcoding kit ###############
+
+[BC%02i]
+compatible_kits = EXP-NBD196,SQK-NBD110-96
+first_index = 1
+last_index = 12
+kit = BC
+normalised_id = barcode%02i
+scoring_function = MAX
+mask1 = JHUAPL_IAV_1st
+barcode1 = BC%02i