fix: use latest patterns

docker/Dockerfile

@@ -8,6 +8,7 @@ RUN apt-get update \
         curl \
         python3.11-dev \
         python3.11-full \
+        procps \
     && rm -rf /var/lib/apt/lists/*
 
 # Install Poetry

longplexpy/multiqc_plugin/modules/lima_longplex/__init__.py

@@ -385,7 +385,7 @@ def __init__(self) -> None:
             },
         }
 
-        self.general_stats_addcols(data=longplex_summary_metrics, headers=headers)
+        self.general_stats_addcols(longplex_summary_metrics, headers=headers)
 
         # Detailed Metrics #############################################################
 
@@ -454,8 +454,8 @@ def __init__(self) -> None:
         }
 
         keys: Dict[str, Dict[str, str]] = {
-            "i7_demuxed": {"name": "ZMWs with i7"},
             "i7_and_i5_demuxed": {"name": "ZMWs with i5 and i7"},
+            "i7_demuxed": {"name": "ZMWs with i7"},
             "i5_demuxed": {"name": "ZMWs with i5"},
             "failed_to_demux": {"name": "ZMWs without i5 or i7"},
         }
@@ -479,9 +479,9 @@ def __init__(self) -> None:
         well_data = [summed_count_metrics[pool].well_counts for pool in pools]
 
         well_keys: Dict[str, Dict[str, str]] = {
-            "P7": {"name": "ZMWs with i7"},
             "P7+P5": {"name": "ZMWs with i5 and i7"},
             "P5+P7": {"name": "ZMWs with i5 and i7"},
+            "P7": {"name": "ZMWs with i7"},
             "P5": {"name": "ZMWs with i5"},
         }
 

tests/data/demux_either_i7_i5/i7_5_bc1015.lima.counts

@@ -0,0 +1,49 @@
+IdxFirst	IdxCombined	IdxFirstNamed	IdxCombinedNamed	Counts	MeanScore
+0	0	seqwell_UDI1_A01_P7	seqwell_UDI1_A01_P7	162	99
+1	1	seqwell_UDI1_B01_P7	seqwell_UDI1_B01_P7	174	98
+2	2	seqwell_UDI1_C01_P7	seqwell_UDI1_C01_P7	160	99
+3	3	seqwell_UDI1_D01_P7	seqwell_UDI1_D01_P7	178	98
+4	4	seqwell_UDI1_E01_P7	seqwell_UDI1_E01_P7	239	99
+5	5	seqwell_UDI1_F01_P7	seqwell_UDI1_F01_P7	44	99
+6	6	seqwell_UDI1_G01_P7	seqwell_UDI1_G01_P7	140	98
+7	7	seqwell_UDI1_H01_P7	seqwell_UDI1_H01_P7	246	99
+8	8	seqwell_UDI1_A02_P7	seqwell_UDI1_A02_P7	143	99
+9	9	seqwell_UDI1_B02_P7	seqwell_UDI1_B02_P7	126	99
+10	10	seqwell_UDI1_C02_P7	seqwell_UDI1_C02_P7	85	99
+11	11	seqwell_UDI1_D02_P7	seqwell_UDI1_D02_P7	138	99
+12	12	seqwell_UDI1_E02_P7	seqwell_UDI1_E02_P7	153	99
+13	13	seqwell_UDI1_F02_P7	seqwell_UDI1_F02_P7	39	99
+14	14	seqwell_UDI1_G02_P7	seqwell_UDI1_G02_P7	127	98
+15	15	seqwell_UDI1_H02_P7	seqwell_UDI1_H02_P7	131	98
+16	16	seqwell_UDI1_A03_P7	seqwell_UDI1_A03_P7	143	99
+17	17	seqwell_UDI1_B03_P7	seqwell_UDI1_B03_P7	153	98
+18	18	seqwell_UDI1_C03_P7	seqwell_UDI1_C03_P7	142	99
+19	19	seqwell_UDI1_D03_P7	seqwell_UDI1_D03_P7	121	99
+20	20	seqwell_UDI1_E03_P7	seqwell_UDI1_E03_P7	93	99
+21	21	seqwell_UDI1_F03_P7	seqwell_UDI1_F03_P7	50	99
+22	22	seqwell_UDI1_G03_P7	seqwell_UDI1_G03_P7	69	98
+23	23	seqwell_UDI1_H03_P7	seqwell_UDI1_H03_P7	157	99
+96	96	seqwell_UDI1_A01_P5	seqwell_UDI1_A01_P5	272	98
+97	97	seqwell_UDI1_B01_P5	seqwell_UDI1_B01_P5	149	98
+98	98	seqwell_UDI1_C01_P5	seqwell_UDI1_C01_P5	142	98
+99	99	seqwell_UDI1_D01_P5	seqwell_UDI1_D01_P5	61	98
+100	100	seqwell_UDI1_E01_P5	seqwell_UDI1_E01_P5	123	99
+101	101	seqwell_UDI1_F01_P5	seqwell_UDI1_F01_P5	68	99
+102	102	seqwell_UDI1_G01_P5	seqwell_UDI1_G01_P5	196	98
+103	103	seqwell_UDI1_H01_P5	seqwell_UDI1_H01_P5	171	98
+104	104	seqwell_UDI1_A02_P5	seqwell_UDI1_A02_P5	314	98
+105	105	seqwell_UDI1_B02_P5	seqwell_UDI1_B02_P5	134	98
+106	106	seqwell_UDI1_C02_P5	seqwell_UDI1_C02_P5	218	98
+107	107	seqwell_UDI1_D02_P5	seqwell_UDI1_D02_P5	105	98
+108	108	seqwell_UDI1_E02_P5	seqwell_UDI1_E02_P5	126	98
+109	109	seqwell_UDI1_F02_P5	seqwell_UDI1_F02_P5	45	99
+110	110	seqwell_UDI1_G02_P5	seqwell_UDI1_G02_P5	172	98
+111	111	seqwell_UDI1_H02_P5	seqwell_UDI1_H02_P5	94	99
+112	112	seqwell_UDI1_A03_P5	seqwell_UDI1_A03_P5	240	98
+113	113	seqwell_UDI1_B03_P5	seqwell_UDI1_B03_P5	116	97
+114	114	seqwell_UDI1_C03_P5	seqwell_UDI1_C03_P5	133	98
+115	115	seqwell_UDI1_D03_P5	seqwell_UDI1_D03_P5	125	98
+116	116	seqwell_UDI1_E03_P5	seqwell_UDI1_E03_P5	158	98
+117	117	seqwell_UDI1_F03_P5	seqwell_UDI1_F03_P5	31	99
+118	118	seqwell_UDI1_G03_P5	seqwell_UDI1_G03_P5	143	99
+119	119	seqwell_UDI1_H03_P5	seqwell_UDI1_H03_P5	90	99

tests/data/demux_either_i7_i5/i7_5_bc1015.lima.summary

@@ -0,0 +1,24 @@
+ZMWs input                (A) : 6881
+ZMWs above all thresholds (B) : 6639 (96.48%)
+ZMWs below any threshold  (C) : 242 (3.52%)
+
+ZMW marginals for (C):
+Below min length              : 0 (0.00%)
+Below min score               : 162 (66.94%)
+Below min end score           : 0 (0.00%)
+Below min passes              : 0 (0.00%)
+Below min score lead          : 242 (100.00%)
+Below min ref span            : 180 (74.38%)
+Without SMRTbell adapter      : 0 (0.00%)
+
+ZMWs for (B):
+With same pair                : 6639 (100.00%)
+Coefficient of correlation    : 43.34%
+
+ZMWs for (A):
+Allow diff pair               : 6881 (100.00%)
+Allow same pair               : 6881 (100.00%)
+
+Reads for (B):
+Above length                  : 6639 (100.00%)
+Below length                  : 0 (0.00%)

tests/data/demux_i7_i5/i7_i5_bc1015.lima.counts

@@ -0,0 +1,25 @@
+IdxFirst	IdxCombined	IdxFirstNamed	IdxCombinedNamed	Counts	MeanScore
+0	1	seqwell_UDI1_A01_P5	seqwell_UDI1_A01_P7	248	98
+2	3	seqwell_UDI1_A02_P5	seqwell_UDI1_A02_P7	243	99
+4	5	seqwell_UDI1_A03_P5	seqwell_UDI1_A03_P7	228	99
+24	25	seqwell_UDI1_B01_P5	seqwell_UDI1_B01_P7	206	99
+26	27	seqwell_UDI1_B02_P5	seqwell_UDI1_B02_P7	123	99
+28	29	seqwell_UDI1_B03_P5	seqwell_UDI1_B03_P7	139	99
+48	49	seqwell_UDI1_C01_P5	seqwell_UDI1_C01_P7	197	98
+50	51	seqwell_UDI1_C02_P5	seqwell_UDI1_C02_P7	192	99
+52	53	seqwell_UDI1_C03_P5	seqwell_UDI1_C03_P7	199	99
+72	73	seqwell_UDI1_D01_P5	seqwell_UDI1_D01_P7	111	98
+74	75	seqwell_UDI1_D02_P5	seqwell_UDI1_D02_P7	122	99
+76	77	seqwell_UDI1_D03_P5	seqwell_UDI1_D03_P7	155	99
+96	97	seqwell_UDI1_E01_P5	seqwell_UDI1_E01_P7	236	99
+98	99	seqwell_UDI1_E02_P5	seqwell_UDI1_E02_P7	193	99
+100	101	seqwell_UDI1_E03_P5	seqwell_UDI1_E03_P7	171	99
+120	121	seqwell_UDI1_F01_P5	seqwell_UDI1_F01_P7	40	99
+122	123	seqwell_UDI1_F02_P5	seqwell_UDI1_F02_P7	30	99
+124	125	seqwell_UDI1_F03_P5	seqwell_UDI1_F03_P7	38	99
+144	145	seqwell_UDI1_G01_P5	seqwell_UDI1_G01_P7	219	99
+146	147	seqwell_UDI1_G02_P5	seqwell_UDI1_G02_P7	179	99
+148	149	seqwell_UDI1_G03_P5	seqwell_UDI1_G03_P7	127	99
+168	169	seqwell_UDI1_H01_P5	seqwell_UDI1_H01_P7	283	99
+170	171	seqwell_UDI1_H02_P5	seqwell_UDI1_H02_P7	147	99
+172	173	seqwell_UDI1_H03_P5	seqwell_UDI1_H03_P7	221	99

tests/data/demux_i7_i5/i7_i5_bc1015.lima.summary

@@ -0,0 +1,26 @@
+ZMWs input                (A) : 11014
+ZMWs above all thresholds (B) : 4047 (36.74%)
+ZMWs below any threshold  (C) : 6967 (63.26%)
+
+ZMW marginals for (C):
+Below min length              : 0 (0.00%)
+Below min score               : 189 (2.71%)
+Below min end score           : 0 (0.00%)
+Below min passes              : 0 (0.00%)
+Below min score lead          : 244 (3.50%)
+Below min ref span            : 179 (2.57%)
+Without SMRTbell adapter      : 0 (0.00%)
+Undesired hybrids             : 86 (1.23%)
+Not direct neighbors          : 6967 (100.00%)
+
+ZMWs for (B):
+With different pair           : 4047 (100.00%)
+Coefficient of correlation    : 39.47%
+
+ZMWs for (A):
+Allow diff pair               : 11014 (100.00%)
+Allow same pair               : 11014 (100.00%)
+
+Reads for (B):
+Above length                  : 4047 (100.00%)
+Below length                  : 0 (0.00%)