diff --git a/snappy_pipeline/workflows/ngs_mapping/Snakefile b/snappy_pipeline/workflows/ngs_mapping/Snakefile
index 929043ea7..25ec76bcc 100644
--- a/snappy_pipeline/workflows/ngs_mapping/Snakefile
+++ b/snappy_pipeline/workflows/ngs_mapping/Snakefile
@@ -117,7 +117,7 @@ rule ngs_mapping_bwa_run:
     log:
         **wf.get_log_file("bwa", "run"),
     wrapper:
-        wf.wrapper_path("bwa")  # TODO => bwa/run
+        wf.wrapper_path("bwa")
 
 
 # Run STAR --------------------------------------------------------------------
@@ -138,7 +138,7 @@ rule ngs_mapping_star_run:
     log:
         **wf.get_log_file("star", "run"),
     wrapper:
-        wf.wrapper_path("star")  # TODO => star/run
+        wf.wrapper_path("star")
 
 
 # GATK-based BAM postprocessing -----------------------------------------------
@@ -158,7 +158,7 @@ if wf.config["postprocessing"] == "gatk_post_bam":
         log:
             **wf.get_log_file("gatk_post_bam", "run"),
         wrapper:
-            wf.wrapper_path("gatk_post_bam")  # TODO => gatk_post_bam/run
+            wf.wrapper_path("gatk_post_bam")
 
 
 # Run minimap2 ---------------------------------------------------------------
@@ -180,48 +180,8 @@ rule ngs_mapping_minimap2_run:
         wf.wrapper_path("minimap2")
 
 
-# Run NGMLR -------------------------------------------------------------------
-
-
-rule ngs_mapping_ngmlr_run:
-    input:
-        wf.get_input_files("ngmlr", "run"),
-    output:
-        **wf.get_output_files("ngmlr", "run"),
-    threads: wf.get_resource("ngmlr", "run", "threads")
-    resources:
-        time=wf.get_resource("ngmlr", "run", "time"),
-        memory=wf.get_resource("ngmlr", "run", "memory"),
-        partition=wf.get_resource("ngmlr", "run", "partition"),
-    params:
-        chained=False,
-    log:
-        **wf.get_log_file("ngmlr", "run"),
-    wrapper:
-        wf.wrapper_path("ngmlr/run")
-
-
 # QC / Statistics ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
-# Generate Picard Hybrid Selection Metrics Report -----------------------------
-
-
-rule ngs_mapping_picard_hs_metrics_run:
-    input:
-        **wf.get_input_files("picard_hs_metrics", "run"),
-    output:
-        **wf.get_output_files("picard_hs_metrics", "run"),
-    threads: wf.get_resource("picard_hs_metrics", "run", "threads")
-    resources:
-        time=wf.get_resource("picard_hs_metrics", "run", "time"),
-        memory=wf.get_resource("picard_hs_metrics", "run", "memory"),
-        partition=wf.get_resource("picard_hs_metrics", "run", "partition"),
-    log:
-        wf.get_log_file("picard_hs_metrics", "run"),
-    wrapper:
-        wf.wrapper_path("picard/hs_metrics")
-
-
 # Generate target region coverage report --------------------------------------
 
 
@@ -238,7 +198,7 @@ rule ngs_mapping_target_coverage_report_run:
     params:
         **{"args": wf.get_params("target_coverage_report", "run")},
     log:
-        wf.get_log_file("target_coverage_report", "run"),
+        **wf.get_log_file("target_coverage_report", "run"),
     wrapper:
         wf.wrapper_path("target_cov_report/run")
 
@@ -284,7 +244,7 @@ rule ngs_mapping_genome_coverage_report_run:
 # Compute depth of coverage files (VCF and bigWig) ----------------------------
 
 
-rule ngs_mapping_generate_doc_files:
+rule ngs_mapping_bam_collect_doc_run:
     input:
         **wf.get_input_files("bam_collect_doc", "run")(),
     output:
@@ -295,6 +255,6 @@ rule ngs_mapping_generate_doc_files:
         memory=wf.get_resource("bam_collect_doc", "run", "memory"),
         partition=wf.get_resource("bam_collect_doc", "run", "partition"),
     log:
-        wf.get_log_file("bam_collect_doc", "run"),
+        **wf.get_log_file("bam_collect_doc", "run"),
     wrapper:
         wf.wrapper_path("maelstrom/bam_collect_doc")
diff --git a/snappy_pipeline/workflows/ngs_mapping/__init__.py b/snappy_pipeline/workflows/ngs_mapping/__init__.py
index 7094339d6..b890222a5 100644
--- a/snappy_pipeline/workflows/ngs_mapping/__init__.py
+++ b/snappy_pipeline/workflows/ngs_mapping/__init__.py
@@ -148,7 +148,6 @@
 
 - (long/PacBio/Nanopore) DNA
     - ``"minimap2"``
-    - ``"ngmlr"``
     - ``"external"``
 
 =======
@@ -313,7 +312,7 @@
 READ_MAPPERS_RNA = ("star",)
 
 #: Available read mappers for (long/PacBio/Nanopoare) DNA-seq data
-READ_MAPPERS_DNA_LONG = ("minialign", "ngmlr", "ngmlr_chained")
+READ_MAPPERS_DNA_LONG = ("minimap2",)
 
 #: Default configuration
 DEFAULT_CONFIG = r"""
@@ -323,7 +322,7 @@
     tools:
       dna: []      # Required if DNA analysis; otherwise, leave empty. Example: 'bwa'.
       rna: []      # Required if RNA analysis; otherwise, leave empty. Example: 'star'.
-      dna_long: [] # Required if long-read mapper used; otherwise, leave empty. Example: 'ngmlr'.
+      dna_long: [] # Required if long-read mapper used; otherwise, leave empty. Example: 'minimap2'.
     path_link_in: ""   # OPTIONAL Override data set configuration search paths for FASTQ files
     # Whether or not to compute coverage BED file
     compute_coverage_bed: false
@@ -345,13 +344,10 @@
       min_cov_warning: 20  # >= 20x for WARNING
       min_cov_ok: 50  # >= 50x for OK
       detailed_reporting: false  # per-exon details (cannot go into multiqc)
+    # Depth of coverage collection, mainly useful for genomes.
     bam_collect_doc:
       enabled: false
       window_length: 1000
-    # Enable Picard HS metrics by setting both paths
-    picard_hs_metrics:
-      path_targets_interval_list: null
-      path_baits_interval_list: null
     # Configuration for BWA
     bwa:
       path_index: REQUIRED # Required if listed in ngs_mapping.tools.dna; otherwise, can be removed.
@@ -391,18 +387,9 @@
       out_sam_strand_field: None # or for cufflinks: intronMotif
       include_unmapped: true
       quant_mode: ''
-    # Configuration for Minialign
-    minialign:
-      # `path_index`: Required if listed in ngs_mapping.tools.dna_long; otherwise, can be removed.
-      path_index: REQUIRED
-      ref_gc_stats: null    # Optional
+    # Configuration for Minimap2
+    minimap2:
       mapping_threads: 16
-      num_threads_bam_view: 4
-    # Configuration for NGMLR
-    ngmlr:
-      # `path_index`: Required if listed in ngs_mapping.tools.dna_long; otherwise, can be removed.
-      path_index: REQUIRED
-      ref_gc_stats: null    # Optional
     # Select postprocessing method, only for DNA alignment
     postprocessing: null # optional, {'gatk_post_bam'}
     # Configuration for GATK BAM postprocessing
@@ -495,13 +482,14 @@ def get_output_files(self, action):
     def _get_log_file(self, action):
         """Return dict of log files."""
         _ = action
-        prefix = "work/{mapper}.{{library_name}}/log/{mapper}.{{library_name}}".format(
-            mapper=self.__class__.name
-        )
+        mapper = self.__class__.name
+        prefix = f"work/{mapper}.{{library_name}}/log/{mapper}.{{library_name}}.mapping"
         key_ext = (
             ("log", ".log"),
             ("conda_info", ".conda_info.txt"),
             ("conda_list", ".conda_list.txt"),
+            ("wrapper", ".wrapper.py"),
+            ("env_yaml", ".environment.yaml"),
         )
         for key, ext in key_ext:
             yield key, prefix + ext
@@ -660,9 +648,9 @@ def get_resource_usage(self, action):
             actions_str = ", ".join(self.actions)
             error_message = f"Action '{action}' is not supported. Valid options: {actions_str}"
             raise UnsupportedActionException(error_message)
-        mem_gb = int(3.5 * self.config["minialign"]["mapping_threads"])
+        mem_gb = int(3.5 * self.config["minimap2"]["mapping_threads"])
         return ResourceUsage(
-            threads=self.config["minialign"]["mapping_threads"],
+            threads=self.config["minimap2"]["mapping_threads"],
             time="2-00:00:00",  # 2 days
             memory=f"{mem_gb}G",
         )
@@ -675,50 +663,6 @@ def _get_params_run(self, wildcards):
         return {"extra_infos": self.parent.ngs_library_to_extra_infos[wildcards.library_name]}
 
 
-class NgmlrStepPart(ReadMappingStepPart):
-    """Support for performing PacBio alignment using NGMLR without chaining"""
-
-    #: Step name
-    name = "ngmlr"
-
-    def check_config(self):
-        """Check parameters in configuration.
-
-        Method checks that all parameters required to execute BWA are present in the
-        configuration. If invalid configuration, it raises InvalidConfiguration exception.
-        """
-        # Check if tool is at all included in workflow
-        if not (set(self.config["tools"]["dna_long"]) & {"ngmlr", "ngmlr_chained"}):
-            return  # NGLMR not run, don't check configuration  # pragma: no cover
-
-        # Check required configuration settings present
-        self.parent.ensure_w_config(
-            config_keys=("step_config", "ngs_mapping", "ngmlr", "path_index"),
-            msg="Path to NGMLR index is required",
-        )
-
-    def get_resource_usage(self, action):
-        """Get Resource Usage
-
-        :param action: Action (i.e., step) in the workflow, example: 'run'.
-        :type action: str
-
-        :return: Returns ResourceUsage for step.
-
-        :raises UnsupportedActionException: if action not in class defined list of valid actions.
-        """
-        if action not in self.actions:
-            actions_str = ", ".join(self.actions)
-            error_message = f"Action '{action}' is not supported. Valid options: {actions_str}"
-            raise UnsupportedActionException(error_message)
-        # TODO: Add resources to DEFAULT_CONFIG instead of hard-coding.
-        return ResourceUsage(
-            threads=16,
-            time="4-00:00:00",  # 4 days
-            memory="50G",
-        )
-
-
 class ExternalStepPart(ReadMappingStepPart):
     """Support for linking in external BAM files"""
 
@@ -846,6 +790,8 @@ def get_log_file(self, action):
             ("log", ".log"),
             ("conda_info", ".conda_info.txt"),
             ("conda_list", ".conda_list.txt"),
+            ("wrapper", ".wrapper.py"),
+            ("env_yaml", ".environment.yaml"),
         )
         for key, ext in key_ext:
             yield key, prefix + ext
@@ -959,60 +905,6 @@ def _get_postproc_token(self):
         }[(do_realignment, do_recalibration)]
 
 
-class PicardHsMetricsStepPart(BaseStepPart):
-    """Build target report from Picard HsMetrics"""
-
-    #: Step name
-    name = "picard_hs_metrics"
-
-    #: Class available actions
-    actions = ("run",)
-
-    def __init__(self, parent):
-        super().__init__(parent)
-
-    @staticmethod
-    def get_input_files(action):
-        """Return required input files"""
-        assert action == "run", "Unsupported action"
-        return {
-            "bam": "work/{mapper_lib}/out/{mapper_lib}.bam",
-            "bai": "work/{mapper_lib}/out/{mapper_lib}.bam.bai",
-        }
-
-    @dictify
-    def get_output_files(self, action):
-        """Return output files"""
-        assert action == "run", "Unsupported action"
-        yield "txt", "work/{mapper_lib}/report/picard_hs_metrics/{mapper_lib}.txt"
-        yield "txt_md5", "work/{mapper_lib}/report/picard_hs_metrics/{mapper_lib}.txt.md5"
-
-    @staticmethod
-    def get_log_file(action):
-        _ = action
-        return "work/{mapper_lib}/log/snakemake.picard_hs_metrics.log"
-
-    def get_resource_usage(self, action):
-        """Get Resource Usage
-
-        :param action: Action (i.e., step) in the workflow, example: 'run'.
-        :type action: str
-
-        :return: Returns ResourceUsage for step.
-
-        :raises UnsupportedActionException: if action not in class defined list of valid actions.
-        """
-        if action not in self.actions:
-            actions_str = ", ".join(self.actions)
-            error_message = f"Action '{action}' is not supported. Valid options: {actions_str}"
-            raise UnsupportedActionException(error_message)
-        return ResourceUsage(
-            threads=2,
-            time="04:00:00",  # 4 hours
-            memory="20G",
-        )
-
-
 class TargetCoverageReportStepPart(BaseStepPart):
     """Build target coverage report"""
 
@@ -1068,12 +960,23 @@ def _get_output_files_collect(self):
         yield "txt", "work/target_cov_report/out/target_cov_report.txt"
         yield "txt_md5", "work/target_cov_report/out/target_cov_report.txt.md5"
 
+    @dictify
     def get_log_file(self, action):
         self._validate_action(action)
         if action == "run":
-            return "work/{mapper_lib}/log/snakemake.target_coverage.log"
+            prefix = "work/{mapper_lib}/log/{mapper_lib}.target_cov_report"
+            key_ext = (
+                ("log", ".log"),
+                ("conda_info", ".conda_info.txt"),
+                ("conda_list", ".conda_list.txt"),
+                ("wrapper", ".wrapper.py"),
+                ("env_yaml", ".environment.yaml"),
+            )
+            for key, ext in key_ext:
+                yield key, prefix + ext
+                yield key + "_md5", prefix + ext + ".md5"
         else:
-            return "work/target_cov_report/log/snakemake.target_coverage.log"
+            yield "log", "work/target_cov_report/log/snakemake.target_coverage.log"
 
     def get_params(self, action):
         assert action == "run", "Parameters only available for action 'run'."
@@ -1254,8 +1157,19 @@ def _get_output_files_run(self):
         yield "bw_md5", "work/{mapper_lib}/report/cov/{mapper_lib}.cov.bw.md5"
 
     @staticmethod
+    @dictify
     def get_log_file(action):
-        return "work/{mapper_lib}/log/snakemake.bam_collect_doc.log"
+        prefix = "work/{mapper_lib}/log/{mapper_lib}.bam_collect_doc"
+        key_ext = (
+            ("log", ".log"),
+            ("conda_info", ".conda_info.txt"),
+            ("conda_list", ".conda_list.txt"),
+            ("wrapper", ".wrapper.py"),
+            ("env_yaml", ".environment.yaml"),
+        )
+        for key, ext in key_ext:
+            yield key, prefix + ext
+            yield key + "_md5", prefix + ext + ".md5"
 
     def get_resource_usage(self, action):
         """Get Resource Usage
@@ -1301,8 +1215,6 @@ def __init__(self, workflow, config, config_lookup_paths, config_paths, workdir)
                 LinkOutBamStepPart,
                 LinkOutStepPart,
                 Minimap2StepPart,
-                NgmlrStepPart,
-                PicardHsMetricsStepPart,
                 StarStepPart,
                 TargetCoverageReportStepPart,
                 BamCollectDocStepPart,
@@ -1369,17 +1281,25 @@ def get_result_files(self):
         yield from self._yield_result_files(
             os.path.join("output", name_pattern, "out", name_pattern + "{ext}"), ext=EXT_VALUES
         )
-        yield from self._yield_result_files(
-            os.path.join("output", name_pattern, "log", "{mapper}.{ngs_library.name}.{ext}"),
-            ext=(
-                "log",
-                "conda_info.txt",
-                "conda_list.txt",
-                "log.md5",
-                "conda_info.txt.md5",
-                "conda_list.txt.md5",
-            ),
-        )
+        infixes = ["mapping", "target_cov_report"]
+        if self.config["bam_collect_doc"]["enabled"]:
+            infixes.append("bam_collect_doc")
+        for infix in infixes:
+            yield from self._yield_result_files(
+                os.path.join("output", name_pattern, "log", "{mapper}.{ngs_library.name}.{ext}"),
+                ext=(
+                    f"{infix}.log",
+                    f"{infix}.conda_info.txt",
+                    f"{infix}.conda_list.txt",
+                    f"{infix}.wrapper.py",
+                    f"{infix}.environment.yaml",
+                    f"{infix}.log.md5",
+                    f"{infix}.conda_info.txt.md5",
+                    f"{infix}.conda_list.txt.md5",
+                    f"{infix}.wrapper.py.md5",
+                    f"{infix}.environment.yaml.md5",
+                ),
+            )
         if self.config["bam_collect_doc"]["enabled"]:
             yield from self._yield_result_files(
                 os.path.join("output", name_pattern, "report", "cov", name_pattern + ".cov.{ext}"),
@@ -1428,20 +1348,6 @@ def get_result_files(self):
                     )
         yield "output/target_cov_report/out/target_cov_report.txt"
         yield "output/target_cov_report/out/target_cov_report.txt.md5"
-        if (
-            self.config["picard_hs_metrics"]["path_targets_interval_list"]
-            and self.config["picard_hs_metrics"]["path_baits_interval_list"]
-        ):
-            yield from self._yield_result_files(
-                os.path.join(
-                    "output", name_pattern, "report", "picard_hs_metrics", name_pattern + ".txt"
-                )
-            )
-            yield from self._yield_result_files(
-                os.path.join(
-                    "output", name_pattern, "report", "picard_hs_metrics", name_pattern + ".txt.md5"
-                )
-            )
         if self.config["compute_coverage_bed"]:
             yield from self._yield_result_files(
                 os.path.join("output", name_pattern, "report", "coverage", name_pattern + "{ext}"),
@@ -1457,7 +1363,7 @@ def _yield_result_files(self, tpl, **kwargs):
         for sheet in self.shortcut_sheets:
             for ngs_library in sheet.all_ngs_libraries:
                 extraction_type = ngs_library.test_sample.extra_infos["extractionType"]
-                if ngs_library.extra_infos["seqPlatform"] in ("ONP", "PacBio"):
+                if ngs_library.extra_infos["seqPlatform"] in ("ONT", "PacBio"):
                     suffix = "_long"
                 else:
                     suffix = ""
diff --git a/snappy_wrappers/wrappers/bwa/__init__.py b/snappy_wrappers/wrappers/bwa/__init__.py
deleted file mode 100644
index 1145fb33d..000000000
--- a/snappy_wrappers/wrappers/bwa/__init__.py
+++ /dev/null
@@ -1,2 +0,0 @@
-# -*- coding: utf-8 -*-
-"""CUBI+Snakemake wrapper for BWA"""
diff --git a/snappy_wrappers/wrappers/bwa/environment.yaml b/snappy_wrappers/wrappers/bwa/environment.yaml
index d8ca1cb6d..8666d5e3d 100644
--- a/snappy_wrappers/wrappers/bwa/environment.yaml
+++ b/snappy_wrappers/wrappers/bwa/environment.yaml
@@ -3,12 +3,10 @@ channels:
   - bioconda
 dependencies:
   - bwa ==0.7.17
-  - samtools ==1.9
-  - samblaster ==0.1.24
+  - samtools =1.16
+  - samblaster ==0.1.26
   - seqtk ==1.3
   - trimadap ==r11
-  # NB: gnuplot 5.2.7 is incompatible with samtools ==1.9
-  # see https://github.com/samtools/samtools/issues/1065
-  - gnuplot ==5.2.6
-  - libpng ==1.6.37
+  - gnuplot ==5.4.5
+  - libpng ==1.6.39
   - inline-html ==1.0.0
diff --git a/snappy_wrappers/wrappers/bwa/wrapper.py b/snappy_wrappers/wrappers/bwa/wrapper.py
index 359cf1097..5a3a5dbac 100644
--- a/snappy_wrappers/wrappers/bwa/wrapper.py
+++ b/snappy_wrappers/wrappers/bwa/wrapper.py
@@ -13,22 +13,20 @@
 input_left = snakemake.params.args["input"]["reads_left"]
 input_right = snakemake.params.args["input"].get("reads_right", "")
 
-this_file = __file__
-
 shell(
     r"""
 set -x
 
-# TODO: remove this again, is for fail early
-# Additional logging for transparency & reproducibility
-# Logging: Save a copy this wrapper (with the pickle details in the header)
-cp {this_file} $(dirname {snakemake.log.log})/wrapper_bwa.py
-
-# Write out information about conda installation.
+# Write out information about conda and save a copy of the wrapper with picked variables
+# as well as the environment.yaml file.
 conda list >{snakemake.log.conda_list}
 conda info >{snakemake.log.conda_info}
 md5sum {snakemake.log.conda_list} >{snakemake.log.conda_list_md5}
 md5sum {snakemake.log.conda_info} >{snakemake.log.conda_info_md5}
+cp {__real_file__} {snakemake.log.wrapper}
+md5sum {snakemake.log.wrapper} >{snakemake.log.wrapper_md5}
+cp $(dirname {__file__})/environment.yaml {snakemake.log.env_yaml}
+md5sum {snakemake.log.env_yaml} >{snakemake.log.env_yaml_md5}
 
 # Also pipe stderr to log file
 if [[ -n "{snakemake.log.log}" ]]; then
@@ -269,6 +267,29 @@
     {snakemake.output.report_bamstats_txt} \
 || true  # ignore failure
 
+# Patch inline-html if necessary.
+cat >$TMPDIR/inline-html.diff <<EOF
+diff --git a/inline_html/inline_html.py b/inline_html/inline_html.py
+index 893086c..cbef6dd 100644
+--- a/inline_html/inline_html.py
++++ b/inline_html/inline_html.py
+@@ -20,7 +20,10 @@ def resource_to_data(path, in_file):
+     mime, _ = mimetypes.guess_type(path)
+     with open(path, 'rb') as fp:
+         data = fp.read()
+-        data64 = b''.join(base64.encodestring(data).splitlines())
++        try:
++            data64 = b''.join(base64.encodestring(data).splitlines())
++        except AttributeError:
++            data64 = b''.join(base64.encodebytes(data).splitlines())
+         return 'data:%s;base64,%s' % (mime, data64.decode('ascii'))
+EOF
+pushd $(python3 -c 'import inline_html; print(inline_html.__path__[0])')
+if ! grep encodebytes inline_html.py; then
+    patch -p2 <$TMPDIR/inline-html.diff
+fi
+popd
+
 # Convert HTML report into one file.
 inline-html \
     --in-file $TMPDIR/bamstats.d/index.html \
@@ -279,19 +300,13 @@
 md5sum {snakemake.output.report_bamstats_txt} > {snakemake.output.report_bamstats_txt_md5}
 md5sum {snakemake.output.report_flagstats_txt} >{snakemake.output.report_flagstats_txt_md5}
 md5sum {snakemake.output.report_idxstats_txt} > {snakemake.output.report_idxstats_txt_md5}
-
-# Additional logging for transparency & reproducibility
-# Logging: Save a copy this wrapper (with the pickle details in the header)
-cp {this_file} $(dirname {snakemake.log.log})/wrapper_bwa.py
-
-# Logging: Save a permanent copy of the environment file used
-cp $(dirname {this_file})/environment.yaml $(dirname {snakemake.log.log})/environment_wrapper_bwa.yaml
 """
 )
 
 # Compute MD5 sums of logs.
 shell(
     r"""
+sleep 1s  # try to wait for log file flush
 md5sum {snakemake.log.log} >{snakemake.log.log_md5}
 """
 )
diff --git a/snappy_wrappers/wrappers/gatk_post_bam/wrapper.py b/snappy_wrappers/wrappers/gatk_post_bam/wrapper.py
index 1330d71d4..0c43e8eda 100644
--- a/snappy_wrappers/wrappers/gatk_post_bam/wrapper.py
+++ b/snappy_wrappers/wrappers/gatk_post_bam/wrapper.py
@@ -22,9 +22,16 @@
     r"""
 set -x
 
-# Write out information about conda installation.
+# Write out information about conda and save a copy of the wrapper with picked variables
+# as well as the environment.yaml file.
 conda list >{snakemake.log.conda_list}
 conda info >{snakemake.log.conda_info}
+md5sum {snakemake.log.conda_list} >{snakemake.log.conda_list_md5}
+md5sum {snakemake.log.conda_info} >{snakemake.log.conda_info_md5}
+cp {__real_file__} {snakemake.log.wrapper}
+md5sum {snakemake.log.wrapper} >{snakemake.log.wrapper_md5}
+cp $(dirname {__file__})/environment.yaml {snakemake.log.env_yaml}
+md5sum {snakemake.log.env_yaml} >{snakemake.log.env_yaml_md5}
 
 # Also pipe stderr to log file
 if [[ -n "{snakemake.log.log}" ]]; then
@@ -178,3 +185,11 @@
 fi
 """
 )
+
+# Compute MD5 sums of logs.
+shell(
+    r"""
+sleep 1s  # try to wait for log file flush
+md5sum {snakemake.log.log} >{snakemake.log.log_md5}
+"""
+)
diff --git a/snappy_wrappers/wrappers/maelstrom/bam_collect_doc/wrapper.py b/snappy_wrappers/wrappers/maelstrom/bam_collect_doc/wrapper.py
index 5bf072efe..dac1e31c2 100644
--- a/snappy_wrappers/wrappers/maelstrom/bam_collect_doc/wrapper.py
+++ b/snappy_wrappers/wrappers/maelstrom/bam_collect_doc/wrapper.py
@@ -6,6 +6,28 @@
     r"""
 set -x
 
+# Write out information about conda and save a copy of the wrapper with picked variables
+# as well as the environment.yaml file.
+conda list >{snakemake.log.conda_list}
+conda info >{snakemake.log.conda_info}
+md5sum {snakemake.log.conda_list} >{snakemake.log.conda_list_md5}
+md5sum {snakemake.log.conda_info} >{snakemake.log.conda_info_md5}
+cp {__real_file__} {snakemake.log.wrapper}
+md5sum {snakemake.log.wrapper} >{snakemake.log.wrapper_md5}
+cp $(dirname {__file__})/environment.yaml {snakemake.log.env_yaml}
+md5sum {snakemake.log.env_yaml} >{snakemake.log.env_yaml_md5}
+
+# Also pipe stderr to log file
+if [[ -n "{snakemake.log.log}" ]]; then
+    if [[ "$(set +e; tty; set -e)" != "" ]]; then
+        rm -f "{snakemake.log.log}" && mkdir -p $(dirname {snakemake.log.log})
+        exec 2> >(tee -a "{snakemake.log.log}" >&2)
+    else
+        rm -f "{snakemake.log.log}" && mkdir -p $(dirname {snakemake.log.log})
+        echo "No tty, logging disabled" >"{snakemake.log.log}"
+    fi
+fi
+
 export TMPDIR=$(mktemp -d)
 trap "rm -rf $TMPDIR" ERR EXIT
 
@@ -47,3 +69,11 @@
 md5sum $(basename {snakemake.output.bw}) >$(basename {snakemake.output.bw_md5})
 """
 )
+
+# Compute MD5 sums of logs.
+shell(
+    r"""
+sleep 1s  # try to wait for log file flush
+md5sum {snakemake.log.log} >{snakemake.log.log_md5}
+"""
+)
diff --git a/snappy_wrappers/wrappers/minimap2/wrapper.py b/snappy_wrappers/wrappers/minimap2/wrapper.py
index d22fdc924..1372918f4 100644
--- a/snappy_wrappers/wrappers/minimap2/wrapper.py
+++ b/snappy_wrappers/wrappers/minimap2/wrapper.py
@@ -15,9 +15,16 @@
     r"""
 set -x
 
-# Write out information about conda installation.
+# Write out information about conda and save a copy of the wrapper with picked variables
+# as well as the environment.yaml file.
 conda list >{snakemake.log.conda_list}
 conda info >{snakemake.log.conda_info}
+md5sum {snakemake.log.conda_list} >{snakemake.log.conda_list_md5}
+md5sum {snakemake.log.conda_info} >{snakemake.log.conda_info_md5}
+cp {__real_file__} {snakemake.log.wrapper}
+md5sum {snakemake.log.wrapper} >{snakemake.log.wrapper_md5}
+cp $(dirname {__file__})/environment.yaml {snakemake.log.env_yaml}
+md5sum {snakemake.log.env_yaml} >{snakemake.log.env_yaml_md5}
 
 # Also pipe stderr to log file
 if [[ -n "{snakemake.log.log}" ]]; then
@@ -107,6 +114,29 @@
     {snakemake.output.report_bamstats_txt} \
 || true  # ignore failure
 
+# Patch inline-html if necessary.
+cat >$TMPDIR/inline-html.diff <<EOF
+diff --git a/inline_html/inline_html.py b/inline_html/inline_html.py
+index 893086c..cbef6dd 100644
+--- a/inline_html/inline_html.py
++++ b/inline_html/inline_html.py
+@@ -20,7 +20,10 @@ def resource_to_data(path, in_file):
+     mime, _ = mimetypes.guess_type(path)
+     with open(path, 'rb') as fp:
+         data = fp.read()
+-        data64 = b''.join(base64.encodestring(data).splitlines())
++        try:
++            data64 = b''.join(base64.encodestring(data).splitlines())
++        except AttributeError:
++            data64 = b''.join(base64.encodebytes(data).splitlines())
+         return 'data:%s;base64,%s' % (mime, data64.decode('ascii'))
+EOF
+pushd $(python3 -c 'import inline_html; print(inline_html.__path__[0])')
+if ! grep encodebytes inline_html.py; then
+    patch -p2 <$TMPDIR/inline-html.diff
+fi
+popd
+
 # Convert HTML report into one file.
 inline-html \
     --in-file $TMPDIR/bamstats.d/index.html \
@@ -118,12 +148,13 @@
 md5sum {snakemake.output.report_bamstats_txt} > {snakemake.output.report_bamstats_txt_md5}
 md5sum {snakemake.output.report_flagstats_txt} >{snakemake.output.report_flagstats_txt_md5}
 md5sum {snakemake.output.report_idxstats_txt} > {snakemake.output.report_idxstats_txt_md5}
+"""
+)
 
-# Additional logging for transparency & reproducibility
-# Logging: Save a copy this wrapper (with the pickle details in the header)
-cp {this_file} $(dirname {snakemake.log.log})/wrapper_bwa.py
-
-# Logging: Save a permanent copy of the environment file used
-cp $(dirname {this_file})/environment.yaml $(dirname {snakemake.log.log})/environment_wrapper_bwa.yaml
+# Compute MD5 sums of logs.
+shell(
+    r"""
+sleep 1s  # try to wait for log file flush
+md5sum {snakemake.log.log} >{snakemake.log.log_md5}
 """
 )
diff --git a/snappy_wrappers/wrappers/ngmlr/run/environment.yaml b/snappy_wrappers/wrappers/ngmlr/run/environment.yaml
deleted file mode 100644
index 2feb54c55..000000000
--- a/snappy_wrappers/wrappers/ngmlr/run/environment.yaml
+++ /dev/null
@@ -1,10 +0,0 @@
-channels:
-- conda-forge
-- bioconda
-- defaults
-dependencies:
-- ngmlr ==0.2.7
-- samtools ==1.9
-- htslib ==1.9
-- pysam ==0.15.3
-- inline-html ==0.1.2
diff --git a/snappy_wrappers/wrappers/ngmlr/run/meta.yaml b/snappy_wrappers/wrappers/ngmlr/run/meta.yaml
deleted file mode 100644
index da144de0f..000000000
--- a/snappy_wrappers/wrappers/ngmlr/run/meta.yaml
+++ /dev/null
@@ -1,4 +0,0 @@
-name: ngmlr
-description: Next Generation Mapper for Long-Read Data
-authors:
-- Manuel Holtgrewe
diff --git a/snappy_wrappers/wrappers/ngmlr/run/wrapper.py b/snappy_wrappers/wrappers/ngmlr/run/wrapper.py
deleted file mode 100644
index 7f438a733..000000000
--- a/snappy_wrappers/wrappers/ngmlr/run/wrapper.py
+++ /dev/null
@@ -1,126 +0,0 @@
-# -*- coding: utf-8 -*-
-"""Wrapper for running NGMLR (PacBio/Nanopore aligner)
-"""
-
-from snakemake.shell import shell
-
-__author__ = "Manuel Holtgrewe"
-__email__ = "manuel.holtgrewe@bih-charite.de"
-
-this_file = __file__
-
-# TODO: write out separate read groups
-
-shell(
-    r"""
-set -x
-
-# Write out information about conda installation.
-conda list >{snakemake.log.conda_list}
-conda info >{snakemake.log.conda_info}
-
-# Also pipe stderr to log file
-if [[ -n "{snakemake.log.log}" ]]; then
-    if [[ "$(set +e; tty; set -e)" != "" ]]; then
-        rm -f "{snakemake.log.log}" && mkdir -p $(dirname {snakemake.log.log})
-        exec 2> >(tee -a "{snakemake.log.log}" >&2)
-    else
-        rm -f "{snakemake.log.log}" && mkdir -p $(dirname {snakemake.log.log})
-        echo "No tty, logging disabled" >"{snakemake.log.log}"
-    fi
-fi
-
-BAM_CHAIN=/fast/users/mholtgr/scratch/build/bamChain/bamChain
-
-export TMPDIR=$(mktemp -d)
-trap "rm -rf $TMPDIR" EXIT
-
-mkdir -p $TMPDIR/out $TMPDIR/chained $TMPDIR/sorted $TMPDIR/sort.tmp
-
-#if [[ "{snakemake.wildcards.library_name}" == *PacBio* ]]; then
-preset=pacbio
-#else
-#    preset=ont
-#fi
-
-i=1
-for fname in $(find $(dirname {snakemake.input}) -name '*.bam' -or -name '*.fast?.gz'); do
-    basename=$(basename $fname .bam)
-
-    if [[ "$fname" == *.bam ]]; then \
-        samtools fastq -F 2048 $fname; \
-    else \
-        zcat $fname; \
-    fi \
-    | ngmlr \
-        -t 16 \
-        -x $preset \
-        -r {snakemake.config[step_config][ngs_mapping][ngmlr][path_index]} \
-        -q /dev/stdin \
-        -o /dev/stdout \
-    | samtools addreplacerg \
-        -r "@RT\tID:{snakemake.wildcards.library_name}.$i\tSM:{snakemake.wildcards.library_name}\tPL:PACBIO" - \
-    | samtools sort -l 9 -n -m 4G -@4 -O BAM \
-    >$TMPDIR/out/$i.bam
-
-    if [[ "{snakemake.params[chained]}" == "True" ]]; then
-        python3 $BAM_CHAIN --minmapq 10 $TMPDIR/out/$i.bam $TMPDIR/chained/$i.bam
-    else
-        mv $TMPDIR/out/$i.bam $TMPDIR/chained/$i.bam
-    fi
-
-    samtools sort -m 4G -@ 3 \
-        -o $TMPDIR/sorted/$i.bam \
-        -T $TMPDIR/sort.tmp/ \
-        $TMPDIR/chained/$i.bam
-
-    let "i=$i+1"
-done
-
-out_bam={snakemake.output.bam}
-
-samtools merge -@ 8 $out_bam $TMPDIR/sorted/*.bam
-
-samtools index $out_bam
-
-# Compute MD5 sums
-pushd $(dirname $out_bam)
-md5sum $(basename $out_bam) >$(basename $out_bam).md5
-md5sum $(basename $out_bam).bai >$(basename $out_bam).bai.md5
-popd
-
-# QC Report ---------------------------------------------------------------------------------------
-
-# gather statistics from BAM file
-# TODO: use pipes for only reading once from disk?
-samtools stats    {snakemake.output.bam} > {snakemake.output.report_bamstats_txt}
-samtools flagstat {snakemake.output.bam} > {snakemake.output.report_flagstats_txt}
-samtools idxstats {snakemake.output.bam} > {snakemake.output.report_idxstats_txt}
-
-# call plot-bamstats
-mkdir $TMPDIR/bamstats.d
-plot-bamstats \
-    -p $TMPDIR/bamstats.d/ \
-    {snakemake.output.report_bamstats_txt} \
-|| true  # ignore failure
-
-# Convert HTML report into one file.
-inline-html \
-    --in-file $TMPDIR/bamstats.d/index.html \
-    --out-file {snakemake.output.report_bamstats_html} \
-|| touch {snakemake.output.report_bamstats_html}
-
-# Build MD5 files for the reports
-md5sum {snakemake.output.report_bamstats_html} > {snakemake.output.report_bamstats_html_md5}
-md5sum {snakemake.output.report_bamstats_txt} > {snakemake.output.report_bamstats_txt_md5}
-md5sum {snakemake.output.report_flagstats_txt} >{snakemake.output.report_flagstats_txt_md5}
-md5sum {snakemake.output.report_idxstats_txt} > {snakemake.output.report_idxstats_txt_md5}
-
-# Additional logging for transparency & reproducibility
-# Logging: Save a copy this wrapper (with the pickle details in the header)
-cp {this_file} $(dirname {snakemake.log.log})/wrapper_bwa.py
-
-# Logging: Save a permanent copy of the environment file used
-cp $(dirname {this_file})/environment.yaml $(dirname {snakemake.log.log})/environment_wrapper_bwa.yaml
-"""
-)
diff --git a/snappy_wrappers/wrappers/picard/hs_metrics/environment.yaml b/snappy_wrappers/wrappers/picard/hs_metrics/environment.yaml
deleted file mode 100644
index 725e3a2c0..000000000
--- a/snappy_wrappers/wrappers/picard/hs_metrics/environment.yaml
+++ /dev/null
@@ -1,6 +0,0 @@
-channels:
-- conda-forge
-- bioconda
-- r
-dependencies:
-- picard ==2.14
diff --git a/snappy_wrappers/wrappers/picard/hs_metrics/wrapper.py b/snappy_wrappers/wrappers/picard/hs_metrics/wrapper.py
deleted file mode 100644
index b22db3a97..000000000
--- a/snappy_wrappers/wrappers/picard/hs_metrics/wrapper.py
+++ /dev/null
@@ -1,32 +0,0 @@
-from snakemake import shell
-
-shell(
-    r"""
-set -x
-
-# Also pipe stderr to log file
-if [[ -n "{snakemake.log}" ]]; then
-    if [[ "$(set +e; tty; set -e)" != "" ]]; then
-        rm -f "{snakemake.log}" && mkdir -p $(dirname {snakemake.log})
-        exec 2> >(tee -a "{snakemake.log}" >&2)
-    else
-        rm -f "{snakemake.log}" && mkdir -p $(dirname {snakemake.log})
-        echo "No tty, logging disabled" >"{snakemake.log}"
-    fi
-fi
-
-picard -Xmx6g -Djava.io.tmpdir=$TMPDIR \
-    CollectHsMetrics \
-    I={snakemake.input.bam} \
-    O={snakemake.output.txt} \
-    R={snakemake.config[static_data_config][reference][path]} \
-    MINIMUM_MAPPING_QUALITY=0 \
-    TARGET_INTERVALS={snakemake.config[step_config][ngs_mapping][picard_hs_metrics][path_targets_interval_list]} \
-    BAIT_INTERVALS={snakemake.config[step_config][ngs_mapping][picard_hs_metrics][path_baits_interval_list]} \
-    VALIDATION_STRINGENCY=SILENT
-
-pushd $(dirname {snakemake.output.txt})
-md5sum $(basename {snakemake.output.txt}) >$(basename {snakemake.output.txt}).md5
-popd
-"""
-)
diff --git a/snappy_wrappers/wrappers/star/wrapper.py b/snappy_wrappers/wrappers/star/wrapper.py
index a3709815a..a90691185 100644
--- a/snappy_wrappers/wrappers/star/wrapper.py
+++ b/snappy_wrappers/wrappers/star/wrapper.py
@@ -13,17 +13,20 @@
 reads_left = snakemake.params.args["input"]["reads_left"]
 reads_right = snakemake.params.args["input"].get("reads_right", "")
 
-this_file = __file__
-
 shell(
     r"""
 set -x
 
-# Write out information about conda installation.
+# Write out information about conda and save a copy of the wrapper with picked variables
+# as well as the environment.yaml file.
 conda list >{snakemake.log.conda_list}
 conda info >{snakemake.log.conda_info}
 md5sum {snakemake.log.conda_list} >{snakemake.log.conda_list_md5}
 md5sum {snakemake.log.conda_info} >{snakemake.log.conda_info_md5}
+cp {__real_file__} {snakemake.log.wrapper}
+md5sum {snakemake.log.wrapper} >{snakemake.log.wrapper_md5}
+cp $(dirname {__file__})/environment.yaml {snakemake.log.env_yaml}
+md5sum {snakemake.log.env_yaml} >{snakemake.log.env_yaml_md5}
 
 # Also pipe stderr to log file
 if [[ -n "{snakemake.log.log}" ]]; then
@@ -206,6 +209,29 @@
     {snakemake.output.report_bamstats_txt} \
 || true  # ignore failure
 
+# Patch inline-html if necessary.
+cat >$TMPDIR/inline-html.diff <<EOF
+diff --git a/inline_html/inline_html.py b/inline_html/inline_html.py
+index 893086c..cbef6dd 100644
+--- a/inline_html/inline_html.py
++++ b/inline_html/inline_html.py
+@@ -20,7 +20,10 @@ def resource_to_data(path, in_file):
+     mime, _ = mimetypes.guess_type(path)
+     with open(path, 'rb') as fp:
+         data = fp.read()
+-        data64 = b''.join(base64.encodestring(data).splitlines())
++        try:
++            data64 = b''.join(base64.encodestring(data).splitlines())
++        except AttributeError:
++            data64 = b''.join(base64.encodebytes(data).splitlines())
+         return 'data:%s;base64,%s' % (mime, data64.decode('ascii'))
+EOF
+pushd $(python3 -c 'import inline_html; print(inline_html.__path__[0])')
+if ! grep encodebytes inline_html.py; then
+    patch -p2 <$TMPDIR/inline-html.diff
+fi
+popd
+
 # Convert HTML report into one file.
 inline-html \
     --in-file $TMPDIR/bamstats.d/index.html \
@@ -234,6 +260,7 @@
 # Compute MD5 sums of logs.
 shell(
     r"""
+sleep 1s  # try to wait for log file flush
 md5sum {snakemake.log.log} >{snakemake.log.log_md5}
 """
 )
diff --git a/snappy_wrappers/wrappers/target_cov_report/run/wrapper.py b/snappy_wrappers/wrappers/target_cov_report/run/wrapper.py
index 5ed15ad38..254c0d51a 100644
--- a/snappy_wrappers/wrappers/target_cov_report/run/wrapper.py
+++ b/snappy_wrappers/wrappers/target_cov_report/run/wrapper.py
@@ -8,22 +8,29 @@
 
 shell.executable("/bin/bash")
 
-
 shell(
     r"""
 set -x
 
-# Hack: get back bin directory of base/root environment.
-export PATH=$PATH:$(dirname $(dirname $(which conda)))/bin
+# Write out information about conda and save a copy of the wrapper with picked variables
+# as well as the environment.yaml file.
+conda list >{snakemake.log.conda_list}
+conda info >{snakemake.log.conda_info}
+md5sum {snakemake.log.conda_list} >{snakemake.log.conda_list_md5}
+md5sum {snakemake.log.conda_info} >{snakemake.log.conda_info_md5}
+cp {__real_file__} {snakemake.log.wrapper}
+md5sum {snakemake.log.wrapper} >{snakemake.log.wrapper_md5}
+cp $(dirname {__file__})/environment.yaml {snakemake.log.env_yaml}
+md5sum {snakemake.log.env_yaml} >{snakemake.log.env_yaml_md5}
 
 # Also pipe stderr to log file
-if [[ -n "{snakemake.log}" ]]; then
+if [[ -n "{snakemake.log.log}" ]]; then
     if [[ "$(set +e; tty; set -e)" != "" ]]; then
-        rm -f "{snakemake.log}" && mkdir -p $(dirname {snakemake.log})
-        exec 2> >(tee -a "{snakemake.log}" >&2)
+        rm -f "{snakemake.log.log}" && mkdir -p $(dirname {snakemake.log.log})
+        exec 2> >(tee -a "{snakemake.log.log}" >&2)
     else
-        rm -f "{snakemake.log}" && mkdir -p $(dirname {snakemake.log})
-        echo "No tty, logging disabled" >"{snakemake.log}"
+        rm -f "{snakemake.log.log}" && mkdir -p $(dirname {snakemake.log.log})
+        echo "No tty, logging disabled" >"{snakemake.log.log}"
     fi
 fi
 
@@ -60,3 +67,11 @@
 md5sum {snakemake.output.txt} > {snakemake.output.txt_md5}
 """
 )
+
+# Compute MD5 sums of logs.
+shell(
+    r"""
+sleep 1s  # try to wait for log file flush
+md5sum {snakemake.log.log} >{snakemake.log.log_md5}
+"""
+)
diff --git a/tests/snappy_pipeline/workflows/common.py b/tests/snappy_pipeline/workflows/common.py
index 951965542..3f7794ccc 100644
--- a/tests/snappy_pipeline/workflows/common.py
+++ b/tests/snappy_pipeline/workflows/common.py
@@ -1,25 +1,41 @@
 """Shared method used in methods."""
 
+import typing
 
-def get_expected_log_files_dict(base_out):
+
+def get_expected_log_files_dict(
+    *, base_out: str, infix: typing.Optional[str] = None, extended: bool = False
+):
     """
     :param base_out: Base path structure for log files. For example, if the expected path for
     the log is 'work/step.path/log/step.conda_info.txt', the argument should be
     'work/step.path/log/step'.
-    :type base_out: str
+    :param infix: Optional infix string.
+    :param extended: Whether to include env_yaml and wrapper in output
 
     :return: Returns dictionary with expected path for log files based on the provided input.
     """
-    # Define expected
+    if infix:
+        infix_dot = f"{infix}."
+    else:
+        infix_dot = ""
     expected = {
-        "conda_info": base_out + ".conda_info.txt",
-        "conda_info_md5": base_out + ".conda_info.txt.md5",
-        "conda_list": base_out + ".conda_list.txt",
-        "conda_list_md5": base_out + ".conda_list.txt.md5",
-        "log": base_out + ".log",
-        "log_md5": base_out + ".log.md5",
+        "conda_info": f"{base_out}.{infix_dot}conda_info.txt",
+        "conda_info_md5": f"{base_out}.{infix_dot}conda_info.txt.md5",
+        "conda_list": f"{base_out}.{infix_dot}conda_list.txt",
+        "conda_list_md5": f"{base_out}.{infix_dot}conda_list.txt.md5",
+        "log": f"{base_out}.{infix_dot}log",
+        "log_md5": f"{base_out}.{infix_dot}log.md5",
     }
-    # Return
+    if extended:
+        expected.update(
+            {
+                "env_yaml": f"{base_out}.{infix_dot}environment.yaml",
+                "env_yaml_md5": f"{base_out}.{infix_dot}environment.yaml.md5",
+                "wrapper": f"{base_out}.{infix_dot}wrapper.py",
+                "wrapper_md5": f"{base_out}.{infix_dot}wrapper.py.md5",
+            }
+        )
     return expected
 
 
@@ -35,10 +51,10 @@ def get_expected_output_vcf_files_dict(base_out):
     """
     # Define expected
     expected = {
-        "vcf": base_out + ".vcf.gz",
-        "vcf_md5": base_out + ".vcf.gz.md5",
-        "tbi": base_out + ".vcf.gz.tbi",
-        "tbi_md5": base_out + ".vcf.gz.tbi.md5",
+        "vcf": f"{base_out}.vcf.gz",
+        "vcf_md5": f"{base_out}.vcf.gz.md5",
+        "tbi": f"{base_out}.vcf.gz.tbi",
+        "tbi_md5": f"{base_out}.vcf.gz.tbi.md5",
     }
     # Return
     return expected
@@ -56,10 +72,10 @@ def get_expected_output_bcf_files_dict(base_out):
     """
     # Define expected
     expected = {
-        "bcf": base_out + ".bcf",
-        "bcf_md5": base_out + ".bcf.md5",
-        "csi": base_out + ".bcf.csi",
-        "csi_md5": base_out + ".bcf.csi.md5",
+        "bcf": f"{base_out}.bcf",
+        "bcf_md5": f"{base_out}.bcf.md5",
+        "csi": f"{base_out}.bcf.csi",
+        "csi_md5": f"{base_out}.bcf.csi.md5",
     }
     # Return
     return expected
diff --git a/tests/snappy_pipeline/workflows/test_workflows_ngs_mapping.py b/tests/snappy_pipeline/workflows/test_workflows_ngs_mapping.py
index 22c5f55cd..ddaf4b6b7 100644
--- a/tests/snappy_pipeline/workflows/test_workflows_ngs_mapping.py
+++ b/tests/snappy_pipeline/workflows/test_workflows_ngs_mapping.py
@@ -269,7 +269,9 @@ def test_bwa_step_part_get_log_file(ngs_mapping_workflow):
     """Tests BaseStepPart.get_log_file()"""
     # Define expected
     expected = get_expected_log_files_dict(
-        base_out="work/bwa.{library_name}/log/bwa.{library_name}"
+        base_out="work/bwa.{library_name}/log/bwa.{library_name}",
+        infix="mapping",
+        extended=True,
     )
     # Get actual
     actual = ngs_mapping_workflow.get_log_file("bwa", "run")
@@ -332,7 +334,9 @@ def test_star_step_part_get_log_file(ngs_mapping_workflow):
     """Tests StarStepPart.get_log_file()"""
     # Define expected
     expected = get_expected_log_files_dict(
-        base_out="work/star.{library_name}/log/star.{library_name}"
+        base_out="work/star.{library_name}/log/star.{library_name}",
+        infix="mapping",
+        extended=True,
     )
     # Get actual
     actual = ngs_mapping_workflow.get_log_file("star", "run")
@@ -395,7 +399,9 @@ def test_minimap2_step_part_get_log_file(ngs_mapping_workflow):
     """Tests Minimap2StepPart.get_log_file()"""
     # Define expected
     expected = get_expected_log_files_dict(
-        base_out="work/minimap2.{library_name}/log/minimap2.{library_name}"
+        base_out="work/minimap2.{library_name}/log/minimap2.{library_name}",
+        infix="mapping",
+        extended=True,
     )
     # Get actual
     actual = ngs_mapping_workflow.get_log_file("minimap2", "run")
@@ -413,69 +419,6 @@ def test_minimap2_step_part_get_resource(ngs_mapping_workflow):
         assert actual == expected, msg_error
 
 
-# Tests for NgmlrStepPart -----------------------------------------------------------------------
-
-
-def test_ngmlr_step_part_get_args(ngs_mapping_workflow):
-    """Tests NgmlrStepPart.get_args()"""
-    # Define expected
-    wildcards = Wildcards(fromdict={"library_name": "P001-N1-DNA1-WGS1"})
-    expected = {
-        "input": {
-            "reads_left": ["work/input_links/P001-N1-DNA1-WGS1/FCXXXXXX/L001/P001_R1.fastq.gz"],
-            "reads_right": ["work/input_links/P001-N1-DNA1-WGS1/FCXXXXXX/L001/P001_R2.fastq.gz"],
-        },
-        "platform": "ILLUMINA",
-        "sample_name": "P001-N1-DNA1-WGS1",
-    }
-    # Get actual and assert
-    actual = ngs_mapping_workflow.get_args("ngmlr", "run")(wildcards)
-    assert actual == expected
-
-
-def test_ngmlr_step_part_get_input_files(ngs_mapping_workflow):
-    """Tests NgmlrStepPart.get_input_files()"""
-    # Define expected
-    wildcards = Wildcards(fromdict={"library_name": "P001-N1-DNA1-WGS1"})
-    expected = "work/input_links/P001-N1-DNA1-WGS1/.done"
-    # Get actual and assert
-    actual = ngs_mapping_workflow.get_input_files("ngmlr", "run")(wildcards)
-    assert actual == expected
-
-
-def test_ngmlr_step_part_get_output_files(ngs_mapping_workflow):
-    """Tests NgmlrStepPart.get_output_files()"""
-    # Define expected
-    bam_base_out = "work/ngmlr.{library_name}/out/ngmlr.{library_name}"
-    report_base_out = "work/ngmlr.{library_name}/report/bam_qc/ngmlr.{library_name}"
-    expected = get_expected_output_files_dict(bam_base_out, report_base_out)
-    # Get actual
-    actual = ngs_mapping_workflow.get_output_files("ngmlr", "run")
-    assert actual == expected
-
-
-def test_ngmlr_step_part_get_log_file(ngs_mapping_workflow):
-    """Tests NgmlrStepPart.get_log_file()"""
-    # Define expected
-    expected = get_expected_log_files_dict(
-        base_out="work/ngmlr.{library_name}/log/ngmlr.{library_name}"
-    )
-    # Get actual
-    actual = ngs_mapping_workflow.get_log_file("ngmlr", "run")
-    assert actual == expected
-
-
-def test_ngmlr_step_part_get_resource(ngs_mapping_workflow):
-    """Tests NgmlrStepPart.get_resource()"""
-    # Define expected
-    expected_dict = {"threads": 16, "time": "4-00:00:00", "memory": "50G", "partition": "medium"}
-    # Evaluate
-    for resource, expected in expected_dict.items():
-        msg_error = f"Assertion error for resource '{resource}'."
-        actual = ngs_mapping_workflow.get_resource("ngmlr", "run", resource)
-        assert actual == expected, msg_error
-
-
 # Tests for ExternalStepPart -----------------------------------------------------------------------
 
 
@@ -554,7 +497,8 @@ def test_gatk_post_bam_step_part_get_output_files(ngs_mapping_workflow):
 def test_gatk_post_bam_step_part_get_log_file(ngs_mapping_workflow):
     """Tests GatkPostBamStepPart.get_log_file()"""
     expected = get_expected_log_files_dict(
-        base_out="work/{mapper}.{library_name}/log/gatk_post_bam.{library_name}"
+        base_out="work/{mapper}.{library_name}/log/gatk_post_bam.{library_name}",
+        extended=True,
     )
     actual = ngs_mapping_workflow.get_log_file("gatk_post_bam", "run")
     assert actual == expected
@@ -621,53 +565,6 @@ def test_link_out_bam_step_part_get_shell_cmd(ngs_mapping_workflow):
     assert actual == expected
 
 
-# Tests for PicardHsMetricsStepPart ----------------------------------------------------------------
-
-
-def test_picard_hs_metrics_step_part_get_input_files(ngs_mapping_workflow):
-    """Tests PicardHsMetricsStepPart.get_input_files()"""
-    # Define expected
-    expected = {
-        "bam": "work/{mapper_lib}/out/{mapper_lib}.bam",
-        "bai": "work/{mapper_lib}/out/{mapper_lib}.bam.bai",
-    }
-    # Get actual and assert
-    actual = ngs_mapping_workflow.get_input_files("picard_hs_metrics", "run")
-    assert actual == expected
-
-
-def test_picard_hs_metrics_step_part_get_output_files(ngs_mapping_workflow):
-    """Tests PicardHsMetricsStepPart.get_output_files()"""
-    # Define expected
-    expected = {
-        "txt": "work/{mapper_lib}/report/picard_hs_metrics/{mapper_lib}.txt",
-        "txt_md5": "work/{mapper_lib}/report/picard_hs_metrics/{mapper_lib}.txt.md5",
-    }
-    # Get actual
-    actual = ngs_mapping_workflow.get_output_files("picard_hs_metrics", "run")
-    assert actual == expected
-
-
-def test_picard_hs_metrics_step_part_get_log_file(ngs_mapping_workflow):
-    """Tests PicardHsMetricsStepPart.get_log_file()"""
-    # Define expected
-    expected = "work/{mapper_lib}/log/snakemake.picard_hs_metrics.log"
-    # Get actual
-    actual = ngs_mapping_workflow.get_log_file("picard_hs_metrics", "run")
-    assert actual == expected
-
-
-def test_picard_hs_metrics_step_part_get_resource(ngs_mapping_workflow):
-    """Tests PicardHsMetricsStepPart.get_resource()"""
-    # Define expected
-    expected_dict = {"threads": 2, "time": "04:00:00", "memory": "20G", "partition": "medium"}
-    # Evaluate
-    for resource, expected in expected_dict.items():
-        msg_error = f"Assertion error for resource '{resource}'."
-        actual = ngs_mapping_workflow.get_resource("picard_hs_metrics", "run", resource)
-        assert actual == expected, msg_error
-
-
 # Tests for TargetCoverageReportStepPart ----------------------------------------------------------
 
 
@@ -712,13 +609,24 @@ def test_target_coverage_report_step_part_get_output_files(ngs_mapping_workflow)
 
 def test_target_coverage_report_step_part_run_get_log_file(ngs_mapping_workflow):
     """Tests TargetCoverageReportStepPart.get_log_file() - run"""
-    expected = "work/{mapper_lib}/log/snakemake.target_coverage.log"
+    expected = {
+        "log": "work/{mapper_lib}/log/{mapper_lib}.target_cov_report.log",
+        "log_md5": "work/{mapper_lib}/log/{mapper_lib}.target_cov_report.log.md5",
+        "conda_info": "work/{mapper_lib}/log/{mapper_lib}.target_cov_report.conda_info.txt",
+        "conda_info_md5": "work/{mapper_lib}/log/{mapper_lib}.target_cov_report.conda_info.txt.md5",
+        "conda_list": "work/{mapper_lib}/log/{mapper_lib}.target_cov_report.conda_list.txt",
+        "conda_list_md5": "work/{mapper_lib}/log/{mapper_lib}.target_cov_report.conda_list.txt.md5",
+        "wrapper": "work/{mapper_lib}/log/{mapper_lib}.target_cov_report.wrapper.py",
+        "wrapper_md5": "work/{mapper_lib}/log/{mapper_lib}.target_cov_report.wrapper.py.md5",
+        "env_yaml": "work/{mapper_lib}/log/{mapper_lib}.target_cov_report.environment.yaml",
+        "env_yaml_md5": "work/{mapper_lib}/log/{mapper_lib}.target_cov_report.environment.yaml.md5",
+    }
     assert ngs_mapping_workflow.get_log_file("target_coverage_report", "run") == expected
 
 
 def test_target_coverage_report_step_part_collect_get_log_file(ngs_mapping_workflow):
     """Tests TargetCoverageReportStepPart.get_log_file() - collect"""
-    expected = "work/target_cov_report/log/snakemake.target_coverage.log"
+    expected = {"log": "work/target_cov_report/log/snakemake.target_coverage.log"}
     assert ngs_mapping_workflow.get_log_file("target_coverage_report", "collect") == expected
 
 
@@ -788,7 +696,18 @@ def test_generate_doc_files_step_part_get_output_files(ngs_mapping_workflow):
 
 def test_generate_doc_files_step_part_run_get_log_file(ngs_mapping_workflow):
     """Tests BamCollectDocStepPart.get_log_file() - run"""
-    expected = "work/{mapper_lib}/log/snakemake.bam_collect_doc.log"
+    expected = {
+        "log": "work/{mapper_lib}/log/{mapper_lib}.bam_collect_doc.log",
+        "log_md5": "work/{mapper_lib}/log/{mapper_lib}.bam_collect_doc.log.md5",
+        "conda_info": "work/{mapper_lib}/log/{mapper_lib}.bam_collect_doc.conda_info.txt",
+        "conda_info_md5": "work/{mapper_lib}/log/{mapper_lib}.bam_collect_doc.conda_info.txt.md5",
+        "conda_list": "work/{mapper_lib}/log/{mapper_lib}.bam_collect_doc.conda_list.txt",
+        "conda_list_md5": "work/{mapper_lib}/log/{mapper_lib}.bam_collect_doc.conda_list.txt.md5",
+        "wrapper": "work/{mapper_lib}/log/{mapper_lib}.bam_collect_doc.wrapper.py",
+        "wrapper_md5": "work/{mapper_lib}/log/{mapper_lib}.bam_collect_doc.wrapper.py.md5",
+        "env_yaml": "work/{mapper_lib}/log/{mapper_lib}.bam_collect_doc.environment.yaml",
+        "env_yaml_md5": "work/{mapper_lib}/log/{mapper_lib}.bam_collect_doc.environment.yaml.md5",
+    }
     assert ngs_mapping_workflow.get_log_file("bam_collect_doc", "run") == expected
 
 
@@ -874,8 +793,6 @@ def test_ngs_mapping_workflow_steps(ngs_mapping_workflow):
         "link_out",
         "link_out_bam",
         "minimap2",
-        "ngmlr",
-        "picard_hs_metrics",
         "star",
         "target_coverage_report",
     ]
@@ -886,26 +803,31 @@ def test_ngs_mapping_workflow_steps(ngs_mapping_workflow):
 def test_ngs_mapping_workflow_files(ngs_mapping_workflow):
     """Tests simple functionality of the workflow: checks if file structure is created according
     to the expected results from the tools, namely: bwa, external, gatk_post_bam,
-    genome_coverage_report, link_in, link_out, link_out_bam, minimap2, ngmlr, picard_hs_metrics,
-    star, target_coverage_report."""
+    genome_coverage_report, link_in, link_out, link_out_bam, minimap2, star, target_coverage_report.
+    """
     # Check result file construction
     expected = [
         "output/bwa.P00{i}-N1-DNA1-WGS1/out/bwa.P00{i}-N1-DNA1-WGS1.{ext}".format(i=i, ext=ext)
         for i in range(1, 7)
         for ext in ("bam", "bam.bai", "bam.md5", "bam.bai.md5")
     ]
-    expected += [
-        "output/bwa.P00{i}-N1-DNA1-WGS1/log/bwa.P00{i}-N1-DNA1-WGS1.{ext}".format(i=i, ext=ext)
-        for i in range(1, 7)
-        for ext in (
-            "log",
-            "conda_info.txt",
-            "conda_list.txt",
-            "log.md5",
-            "conda_info.txt.md5",
-            "conda_list.txt.md5",
-        )
-    ]
+    for infix in ("bam_collect_doc", "mapping", "target_cov_report"):
+        expected += [
+            "output/bwa.P00{i}-N1-DNA1-WGS1/log/bwa.P00{i}-N1-DNA1-WGS1.{ext}".format(i=i, ext=ext)
+            for i in range(1, 7)
+            for ext in (
+                f"{infix}.log",
+                f"{infix}.log.md5",
+                f"{infix}.conda_info.txt",
+                f"{infix}.conda_info.txt.md5",
+                f"{infix}.conda_list.txt",
+                f"{infix}.conda_list.txt.md5",
+                f"{infix}.environment.yaml",
+                f"{infix}.environment.yaml.md5",
+                f"{infix}.wrapper.py",
+                f"{infix}.wrapper.py.md5",
+            )
+        ]
     bam_stats_text_out = (
         "output/bwa.P00{i}-N1-DNA1-WGS1/report/bam_qc/bwa.P00{i}-N1-DNA1-WGS1.bam.{stats}.{ext}"
     )
diff --git a/tests/snappy_pipeline/workflows/test_workflows_ngs_mapping_processed_fastq.py b/tests/snappy_pipeline/workflows/test_workflows_ngs_mapping_processed_fastq.py
index 375b95662..25c197368 100644
--- a/tests/snappy_pipeline/workflows/test_workflows_ngs_mapping_processed_fastq.py
+++ b/tests/snappy_pipeline/workflows/test_workflows_ngs_mapping_processed_fastq.py
@@ -271,7 +271,9 @@ def test_bwa_step_part_get_log_file(ngs_mapping_workflow):
     """Tests BaseStepPart.get_log_file()"""
     # Define expected
     expected = get_expected_log_files_dict(
-        base_out="work/bwa.{library_name}/log/bwa.{library_name}"
+        base_out="work/bwa.{library_name}/log/bwa.{library_name}",
+        infix="mapping",
+        extended=True,
     )
     # Get actual
     actual = ngs_mapping_workflow.get_log_file("bwa", "run")
@@ -336,7 +338,9 @@ def test_star_step_part_get_log_file(ngs_mapping_workflow):
     """Tests StarStepPart.get_log_file()"""
     # Define expected
     expected = get_expected_log_files_dict(
-        base_out="work/star.{library_name}/log/star.{library_name}"
+        base_out="work/star.{library_name}/log/star.{library_name}",
+        infix="mapping",
+        extended=True,
     )
     # Get actual
     actual = ngs_mapping_workflow.get_log_file("star", "run")
@@ -401,7 +405,9 @@ def test_minimap2_step_part_get_log_file(ngs_mapping_workflow):
     """Tests Minimap2StepPart.get_log_file()"""
     # Define expected
     expected = get_expected_log_files_dict(
-        base_out="work/minimap2.{library_name}/log/minimap2.{library_name}"
+        base_out="work/minimap2.{library_name}/log/minimap2.{library_name}",
+        infix="mapping",
+        extended=True,
     )
     # Get actual
     actual = ngs_mapping_workflow.get_log_file("minimap2", "run")
@@ -419,71 +425,6 @@ def test_minimap2_step_part_get_resource(ngs_mapping_workflow):
         assert actual == expected, msg_error
 
 
-# Tests for NgmlrStepPart -----------------------------------------------------------------------
-
-
-def test_ngmlr_step_part_get_args(ngs_mapping_workflow):
-    """Tests NgmlrStepPart.get_args()"""
-    # Define expected
-    wildcards = Wildcards(fromdict={"library_name": "P001-N1-DNA1-WGS1"})
-    expected = {
-        "input": {
-            "reads_left": ["work/input_links/P001-N1-DNA1-WGS1/FCXXXXXX/L001/out/P001_R1.fastq.gz"],
-            "reads_right": [
-                "work/input_links/P001-N1-DNA1-WGS1/FCXXXXXX/L001/out/P001_R2.fastq.gz"
-            ],
-        },
-        "platform": "ILLUMINA",
-        "sample_name": "P001-N1-DNA1-WGS1",
-    }
-    # Get actual and assert
-    actual = ngs_mapping_workflow.get_args("ngmlr", "run")(wildcards)
-    assert actual == expected
-
-
-def test_ngmlr_step_part_get_input_files(ngs_mapping_workflow):
-    """Tests NgmlrStepPart.get_input_files()"""
-    # Define expected
-    wildcards = Wildcards(fromdict={"library_name": "P001-N1-DNA1-WGS1"})
-    expected = "work/input_links/P001-N1-DNA1-WGS1/.done"
-    # Get actual and assert
-    actual = ngs_mapping_workflow.get_input_files("ngmlr", "run")(wildcards)
-    assert actual == expected
-
-
-def test_ngmlr_step_part_get_output_files(ngs_mapping_workflow):
-    """Tests NgmlrStepPart.get_output_files()"""
-    # Define expected
-    bam_base_out = "work/ngmlr.{library_name}/out/ngmlr.{library_name}"
-    report_base_out = "work/ngmlr.{library_name}/report/bam_qc/ngmlr.{library_name}"
-    expected = get_expected_output_files_dict(bam_base_out, report_base_out)
-    # Get actual
-    actual = ngs_mapping_workflow.get_output_files("ngmlr", "run")
-    assert actual == expected
-
-
-def test_ngmlr_step_part_get_log_file(ngs_mapping_workflow):
-    """Tests NgmlrStepPart.get_log_file()"""
-    # Define expected
-    expected = get_expected_log_files_dict(
-        base_out="work/ngmlr.{library_name}/log/ngmlr.{library_name}"
-    )
-    # Get actual
-    actual = ngs_mapping_workflow.get_log_file("ngmlr", "run")
-    assert actual == expected
-
-
-def test_ngmlr_step_part_get_resource(ngs_mapping_workflow):
-    """Tests NgmlrStepPart.get_resource()"""
-    # Define expected
-    expected_dict = {"threads": 16, "time": "4-00:00:00", "memory": "50G", "partition": "medium"}
-    # Evaluate
-    for resource, expected in expected_dict.items():
-        msg_error = f"Assertion error for resource '{resource}'."
-        actual = ngs_mapping_workflow.get_resource("ngmlr", "run", resource)
-        assert actual == expected, msg_error
-
-
 # Tests for ExternalStepPart -----------------------------------------------------------------------
 
 
@@ -562,7 +503,8 @@ def test_gatk_post_bam_step_part_get_output_files(ngs_mapping_workflow):
 def test_gatk_post_bam_step_part_get_log_file(ngs_mapping_workflow):
     """Tests GatkPostBamStepPart.get_log_file()"""
     expected = get_expected_log_files_dict(
-        base_out="work/{mapper}.{library_name}/log/gatk_post_bam.{library_name}"
+        base_out="work/{mapper}.{library_name}/log/gatk_post_bam.{library_name}",
+        extended=True,
     )
     actual = ngs_mapping_workflow.get_log_file("gatk_post_bam", "run")
     assert actual == expected
@@ -629,53 +571,6 @@ def test_link_out_bam_step_part_get_shell_cmd(ngs_mapping_workflow):
     assert actual == expected
 
 
-# Tests for PicardHsMetricsStepPart ----------------------------------------------------------------
-
-
-def test_picard_hs_metrics_step_part_get_input_files(ngs_mapping_workflow):
-    """Tests PicardHsMetricsStepPart.get_input_files()"""
-    # Define expected
-    expected = {
-        "bam": "work/{mapper_lib}/out/{mapper_lib}.bam",
-        "bai": "work/{mapper_lib}/out/{mapper_lib}.bam.bai",
-    }
-    # Get actual and assert
-    actual = ngs_mapping_workflow.get_input_files("picard_hs_metrics", "run")
-    assert actual == expected
-
-
-def test_picard_hs_metrics_step_part_get_output_files(ngs_mapping_workflow):
-    """Tests PicardHsMetricsStepPart.get_output_files()"""
-    # Define expected
-    expected = {
-        "txt": "work/{mapper_lib}/report/picard_hs_metrics/{mapper_lib}.txt",
-        "txt_md5": "work/{mapper_lib}/report/picard_hs_metrics/{mapper_lib}.txt.md5",
-    }
-    # Get actual
-    actual = ngs_mapping_workflow.get_output_files("picard_hs_metrics", "run")
-    assert actual == expected
-
-
-def test_picard_hs_metrics_step_part_get_log_file(ngs_mapping_workflow):
-    """Tests PicardHsMetricsStepPart.get_log_file()"""
-    # Define expected
-    expected = "work/{mapper_lib}/log/snakemake.picard_hs_metrics.log"
-    # Get actual
-    actual = ngs_mapping_workflow.get_log_file("picard_hs_metrics", "run")
-    assert actual == expected
-
-
-def test_picard_hs_metrics_step_part_get_resource(ngs_mapping_workflow):
-    """Tests PicardHsMetricsStepPart.get_resource()"""
-    # Define expected
-    expected_dict = {"threads": 2, "time": "04:00:00", "memory": "20G", "partition": "medium"}
-    # Evaluate
-    for resource, expected in expected_dict.items():
-        msg_error = f"Assertion error for resource '{resource}'."
-        actual = ngs_mapping_workflow.get_resource("picard_hs_metrics", "run", resource)
-        assert actual == expected, msg_error
-
-
 # Tests for TargetCoverageReportStepPart ----------------------------------------------------------
 
 
@@ -721,12 +616,24 @@ def test_target_coverage_report_step_part_get_output_files(ngs_mapping_workflow)
 def test_target_coverage_report_step_part_run_get_log_file(ngs_mapping_workflow):
     """Tests TargetCoverageReportStepPart.get_log_file() - run"""
     expected = "work/{mapper_lib}/log/snakemake.target_coverage.log"
+    expected = {
+        "log": "work/{mapper_lib}/log/{mapper_lib}.target_cov_report.log",
+        "log_md5": "work/{mapper_lib}/log/{mapper_lib}.target_cov_report.log.md5",
+        "conda_info": "work/{mapper_lib}/log/{mapper_lib}.target_cov_report.conda_info.txt",
+        "conda_info_md5": "work/{mapper_lib}/log/{mapper_lib}.target_cov_report.conda_info.txt.md5",
+        "conda_list": "work/{mapper_lib}/log/{mapper_lib}.target_cov_report.conda_list.txt",
+        "conda_list_md5": "work/{mapper_lib}/log/{mapper_lib}.target_cov_report.conda_list.txt.md5",
+        "wrapper": "work/{mapper_lib}/log/{mapper_lib}.target_cov_report.wrapper.py",
+        "wrapper_md5": "work/{mapper_lib}/log/{mapper_lib}.target_cov_report.wrapper.py.md5",
+        "env_yaml": "work/{mapper_lib}/log/{mapper_lib}.target_cov_report.environment.yaml",
+        "env_yaml_md5": "work/{mapper_lib}/log/{mapper_lib}.target_cov_report.environment.yaml.md5",
+    }
     assert ngs_mapping_workflow.get_log_file("target_coverage_report", "run") == expected
 
 
 def test_target_coverage_report_step_part_collect_get_log_file(ngs_mapping_workflow):
     """Tests TargetCoverageReportStepPart.get_log_file() - collect"""
-    expected = "work/target_cov_report/log/snakemake.target_coverage.log"
+    expected = {"log": "work/target_cov_report/log/snakemake.target_coverage.log"}
     assert ngs_mapping_workflow.get_log_file("target_coverage_report", "collect") == expected
 
 
@@ -817,8 +724,6 @@ def test_ngs_mapping_workflow_steps(ngs_mapping_workflow):
         "link_out",
         "link_out_bam",
         "minimap2",
-        "ngmlr",
-        "picard_hs_metrics",
         "star",
         "target_coverage_report",
     ]
@@ -829,26 +734,31 @@ def test_ngs_mapping_workflow_steps(ngs_mapping_workflow):
 def test_ngs_mapping_workflow_files(ngs_mapping_workflow):
     """Tests simple functionality of the workflow: checks if file structure is created according
     to the expected results from the tools, namely: bwa, external, gatk_post_bam,
-    genome_coverage_report, link_in, link_out, link_out_bam, minimap2, ngmlr, picard_hs_metrics,
-    star, target_coverage_report."""
+    genome_coverage_report, link_in, link_out, link_out_bam, minimap2, star, target_coverage_report.
+    """
     # Check result file construction
     expected = [
         "output/bwa.P00{i}-N1-DNA1-WGS1/out/bwa.P00{i}-N1-DNA1-WGS1.{ext}".format(i=i, ext=ext)
         for i in range(1, 7)
         for ext in ("bam", "bam.bai", "bam.md5", "bam.bai.md5")
     ]
-    expected += [
-        "output/bwa.P00{i}-N1-DNA1-WGS1/log/bwa.P00{i}-N1-DNA1-WGS1.{ext}".format(i=i, ext=ext)
-        for i in range(1, 7)
-        for ext in (
-            "log",
-            "conda_info.txt",
-            "conda_list.txt",
-            "log.md5",
-            "conda_info.txt.md5",
-            "conda_list.txt.md5",
-        )
-    ]
+    for infix in ("bam_collect_doc", "mapping", "target_cov_report"):
+        expected += [
+            "output/bwa.P00{i}-N1-DNA1-WGS1/log/bwa.P00{i}-N1-DNA1-WGS1.{ext}".format(i=i, ext=ext)
+            for i in range(1, 7)
+            for ext in (
+                f"{infix}.log",
+                f"{infix}.log.md5",
+                f"{infix}.conda_info.txt",
+                f"{infix}.conda_info.txt.md5",
+                f"{infix}.conda_list.txt",
+                f"{infix}.conda_list.txt.md5",
+                f"{infix}.environment.yaml",
+                f"{infix}.environment.yaml.md5",
+                f"{infix}.wrapper.py",
+                f"{infix}.wrapper.py.md5",
+            )
+        ]
     bam_stats_text_out = (
         "output/bwa.P00{i}-N1-DNA1-WGS1/report/bam_qc/bwa.P00{i}-N1-DNA1-WGS1.bam.{stats}.{ext}"
     )
diff --git a/tests/snappy_pipeline/workflows/test_workflows_somatic_hla_loh_calling.py b/tests/snappy_pipeline/workflows/test_workflows_somatic_hla_loh_calling.py
index 7bfb24790..f82881af0 100644
--- a/tests/snappy_pipeline/workflows/test_workflows_somatic_hla_loh_calling.py
+++ b/tests/snappy_pipeline/workflows/test_workflows_somatic_hla_loh_calling.py
@@ -111,7 +111,7 @@ def test_lohhla_step_part_get_log_file(somatic_hla_loh_calling_workflow):
         "work/{mapper}.{hla_caller}.lohhla.{tumor_library}/log/"
         "{mapper}.{hla_caller}.lohhla.{tumor_library}"
     )
-    expected = get_expected_log_files_dict(base_name_log)
+    expected = get_expected_log_files_dict(base_out=base_name_log)
     actual = somatic_hla_loh_calling_workflow.get_log_file("lohhla", "run")
     assert actual == expected
 
diff --git a/tests/snappy_pipeline/workflows/test_workflows_variant_export_external.py b/tests/snappy_pipeline/workflows/test_workflows_variant_export_external.py
index 3545920b0..a7930569a 100644
--- a/tests/snappy_pipeline/workflows/test_workflows_variant_export_external.py
+++ b/tests/snappy_pipeline/workflows/test_workflows_variant_export_external.py
@@ -233,7 +233,7 @@ def test_bam_reports_step_part_call_get_log_file_bam_qc(
 ):
     """Tests BamReportsExternalStepPart._get_log_file_bam_qc()"""
     base_out = "work/{mapper_lib}/log/{mapper_lib}.bam_qc"
-    expected = get_expected_log_files_dict(base_out)
+    expected = get_expected_log_files_dict(base_out=base_out)
     actual = variant_export_external_workflow.get_log_file("bam_reports", "bam_qc")
     assert actual == expected